[English] 日本語
Yorodumi
- PDB-6s5g: Non-square conformation of KtrA A80P mutant ring with bound ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5g
TitleNon-square conformation of KtrA A80P mutant ring with bound ADP
ComponentsKtr system potassium uptake protein A
KeywordsTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / adp
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.33 Å
AuthorsTeixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
CitationJournal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,96016
Polymers199,5428
Non-polymers3,4188
Water0
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
hetero molecules

E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,96016
Polymers199,5428
Non-polymers3,4188
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)85.335, 132.925, 203.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24942.797 Da / Num. of mol.: 8 / Mutation: A80P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 100mM HEPES-NaOH pH 7.5, 2% PEG 4000, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 4.33→49.28 Å / Num. obs: 14674 / % possible obs: 91.9 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.072 / Rrim(I) all: 0.205 / Net I/σ(I): 7.9
Reflection shellResolution: 4.33→4.84 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3464 / CC1/2: 0.873 / Rpim(I) all: 0.263 / Rrim(I) all: 0.614 / % possible all: 79.1

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j90
Resolution: 4.33→49.28 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 35.22
RfactorNum. reflection% reflection
Rfree0.3143 2650 10 %
Rwork0.2537 --
obs0.2597 14674 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.33→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13528 0 216 0 13744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313976
X-RAY DIFFRACTIONf_angle_d0.72918936
X-RAY DIFFRACTIONf_dihedral_angle_d13.8735224
X-RAY DIFFRACTIONf_chiral_restr0.0272192
X-RAY DIFFRACTIONf_plane_restr0.0032384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3288-4.40750.35741000.3587911X-RAY DIFFRACTION63
4.4075-4.49220.36891270.31971062X-RAY DIFFRACTION76
4.4922-4.58390.3281170.33131025X-RAY DIFFRACTION74
4.5839-4.68350.40911150.31271075X-RAY DIFFRACTION76
4.6835-4.79230.38831160.31921048X-RAY DIFFRACTION74
4.7923-4.91210.37861040.33141050X-RAY DIFFRACTION74
4.9121-5.04470.34561260.31811040X-RAY DIFFRACTION74
5.0447-5.1930.39741360.31911226X-RAY DIFFRACTION89
5.193-5.36040.40891500.31251441X-RAY DIFFRACTION99
5.3604-5.55180.35821380.30181384X-RAY DIFFRACTION99
5.5518-5.77370.33571710.30261406X-RAY DIFFRACTION99
5.7737-6.03610.37411460.28071400X-RAY DIFFRACTION100
6.0361-6.35370.3151340.27791420X-RAY DIFFRACTION100
6.3537-6.75080.32371530.25261398X-RAY DIFFRACTION99
6.7508-7.27060.33791610.25581407X-RAY DIFFRACTION100
7.2706-7.99940.29671800.22021397X-RAY DIFFRACTION100
7.9994-9.15060.221500.17481398X-RAY DIFFRACTION99
9.1506-11.50450.21721530.16171402X-RAY DIFFRACTION99
11.5045-49.28430.30081730.22611373X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.9871-2.00120.54449.425-2.10621.01250.6770.1652-1.3514-1.5274-0.59961.09420.3610.35670.05080.60760.1581-0.09491.6155-0.16680.8501-11.0633-5.9301-17.1603
29.0485-6.1959-8.06527.79116.14742.08140.78750.4678-0.2943-0.4876-0.41710.1466-1.1939-0.9632-0.70540.5910.10450.1180.79060.33170.6736-0.45981.6348-19.1137
33.42571.2031-1.3425.59652.03581.7297-0.3353-0.8315-0.0830.58310.6755-0.17081.08791.2623-0.27421.14260.4236-0.05251.38730.71311.95490.383410.4061-16.785
47.5394-3.41155.3396.6202-0.93544.36360.821-0.2612.03760.6026-1.0423-0.36790.4439-0.07350.16590.6463-0.18320.0051.3428-0.1691.2048-18.461321.8158-9.865
52.3699-1.0286-2.46310.57561.77629.8895-0.06230.29062.2801-0.6571-0.4865-1.1105-2.2684-0.9247-0.14161.4048-0.1062-0.10740.6222-0.09640.7452-30.55128.3569-9.1552
67.72386.67952.54818.59883.01591.07050.59521.35610.04410.3934-0.7514-0.1739-0.1078-1.01410.10271.30630.38560.26612.45790.26810.8511-36.978136.2425-13.986
70.43890.18090.5937-0.01050.15240.72290.4874-0.1835-0.41750.3075-0.07290.1487-0.4488-1.2328-0.36791.8354-0.3935-0.07872.5108-0.21370.7903-40.143524.1736-13.7669
84.23234.3243.47939.45772.97882.9226-1.7222-0.42850.25830.3069-1.1518-0.21540.28510.88051.13890.494-0.53931.06371.9640.7334-0.5484-27.118733.2047-11.5483
92.91451.6179-3.94735.73271.2228.1402-0.0183-2.1436-0.04471.04930.0109-1.7191-0.36252.2453-0.11721.1595-0.2475-0.31151.83520.10930.7844-6.936819.93196.0167
103.69780.3296-3.31024.97661.86672.2671-0.3909-0.0345-0.65520.95091.62770.2759-0.427-0.6454-0.95011.24450.252-0.03111.03920.14790.425-18.828310.37163.5968
115.76282.8412-2.50354.41921.64475.63910.1997-1.2681-0.0151-0.4005-0.9912-0.26280.66431.52860.64471.27170.2948-0.01491.42690.09680.6201-24.640420.6494-31.2723
129.31844.1504-4.72922.0683-1.22513.99860.187-1.1809-0.78890.84690.23471.02460.59130.45650.00331.7324-0.17610.23780.99750.35670.6308-28.705413.4221-29.5921
132.3761-0.948-1.07257.5327-4.86495.39870.7748-0.1970.57781.16150.35661.05-0.8175-0.3063-0.45831.28690.5794-0.4684-0.8675-0.05150.9125-23.800314.2545-70.2544
145.7409-3.0368-4.73784.06461.5686.9239-0.6061.522-0.5310.1551-0.49950.6150.8058-1.2440.60611.59810.3855-0.51080.5648-0.07910.9896-32.76913.5524-77.2909
157.95930.56463.11918.3882-0.58346.4834-0.16161.18291.3418-1.23950.3835-0.4868-0.548-0.18350.09321.0269-1.0128-0.66780.8854-0.30560.9747-23.61310.9305-81.0308
165.09440.0274.36071.27441.3254.8226-0.10611.55890.9467-1.1555-0.1945-0.4803-0.0039-0.35480.26891.1607-1.10690.01040.6412-0.58591.4707-21.5014.2041-83.1272
176.1511-1.6290.64250.50170.70352.0574-0.2677-0.1365-0.6419-0.354-0.00640.03330.29210.70130.24041.11720.7499-0.84341.1383-0.06361.5959-15.0552-1.407-79.8754
181.557-3.65592.05241.98571.96432.0125-0.37421.18460.36490.2631-0.2458-0.3116-0.49980.35160.4740.94830.2826-0.04991.08360.39121.5148-11.21790.5039-59.9968
192.48711.50522.93252.2429-1.08648.921-0.67830.7384-1.1237-0.41850.5065-0.84121.4441-0.76270.4071.5346-0.16620.02961.334-0.25640.88330.51189.0744-49.2971
201.52093.1224-0.85169.0934-2.1254.84410.24850.014-0.1460.8246-1.1202-0.7096-0.0262.00260.70241.19740.8502-0.22192.1584-0.34040.93782.401413.1145-47.393
219.3175-4.139-3.69117.2372.76427.4546-0.7046-0.1133-1.5585-0.1310.0786-1.05411.09630.99610.70230.64510.00390.07780.63990.1161.0432-19.3289-12.0043-54.7921
222.827-0.8695-0.77615.1087-2.35922.1410.2902-2.3502-0.6262-0.13151.1843-1.4333-1.3526-0.3854-0.91930.6664-0.03170.0430.8406-0.09660.9171-22.37864.3549-55.2536
233.45690.6155-1.00216.00211.31726.6835-0.071-0.5657-0.359-0.85270.58970.71220.12880.1576-0.72951.11150.2987-0.06521.10060.41071.10140.742520.6304-66.8636
241.9720.5612-1.69922.13322.41865.7058-0.4924-0.8726-0.6236-0.73780.58980.2996-1.79640.3345-0.23431.0910.16280.27891.38420.35681.22570.841523.2053-67.862
254.59482.0079-1.52833.116-2.52193.84930.7375-0.5051.53170.13250.6241.36640.0381-0.4222-0.71740.8999-0.220.63650.09751.15940.7871-37.127549.5134-35.2122
261.99922.16996.35796.5997-0.87633.93471.0479-1.66551.00261.49490.75730.77580.1987-0.4054-1.35941.4027-0.17920.55392.0967-0.07520.9598-36.327853.1652-20.7912
274.2641-1.3082-2.41056.4715-0.75595.96660.2708-0.6539-0.83270.11870.1755-0.16580.92810.30220.0440.25980.78071.07271.79880.1567-0.3375-28.948552.8941-27.8729
281.72221.0741.48832.71840.35053.5472-1.9338-1.13741.0027-0.31290.97311.1588-0.77051.2270.1531-0.6879-0.64350.5692.3058-0.01660.8206-23.971962.1881-34.6334
292.0443-1.44718.65887.459-3.09372.04460.95592.25980.8045-0.65211.24740.7436-1.12990.1229-1.43951.5789-0.4433-0.1072.3202-0.0890.5477-18.926758.7069-57.6011
307.8477-2.60681.02527.0289-0.95979.93222.23430.559-0.1659-1.8593-0.437-0.4723-0.433-0.4651-1.75211.32650.12590.18591.19270.03120.7193-18.154550.1254-70.6634
314.11794.8089-2.36237.968-2.78681.3472-0.95340.59820.95160.2840.62250.0785-0.8750.59410.4561.32660.0978-0.29721.20610.23431.304-14.393259.0441-65.8312
325.68811.53021.63538.4051-4.48653.53010.2217-0.57520.19640.1738-0.3695-2.12780.00861.37180.23520.73890.41260.16230.97120.02390.8431-27.054872.5313-52.2588
336.5261-0.8038-0.02623.5089-0.23690.0350.3031-0.7280.70920.6756-0.0553-0.8318-0.5169-0.3022-0.09380.8182-0.93130.22011.0754-0.72221.4076-28.848280.4857-49.4061
340.09440.4043-0.02581.7839-0.11220.0021-0.09720.08480.89761.285-0.27740.8406-0.25650.563-0.02942.0562-0.4176-0.2522-0.20020.21340.9932-40.928882.9562-54.2904
358.01381.6139-2.83812.2771-6.76332.03150.35250.55170.6397-0.8752-0.1341-1.15730.1766-0.11940.17430.8840.44910.02021.38440.38510.9394-37.127973.8866-57.0262
363.97531.4285-3.7562.747-1.04483.5704-0.13760.80170.5606-0.5123-0.21060.0843-0.8133-0.33640.24720.8149-0.1461-0.70731.871-0.39010.4207-46.107271.6913-54.561
374.858-2.6295-0.7717.38012.15862.5452-0.20240.3146-0.1323-0.61760.18770.02240.8619-0.7265-0.28140.71441.1654-0.55671.84071.1515-1.8888-39.374567.4459-56.9516
381.3357-0.82222.43864.4459-0.94766.57480.9358-0.1577-1.4041-0.5804-0.8850.7932-0.6588-1.9523-0.09490.73930.14280.31331.2053-0.00931.4429-37.046457.1869-49.9238
398.0831-0.0818-1.65049.90631.59330.5843-0.4257-0.1594-1.84391.1582-0.53371.5027-0.6889-0.98450.6760.80231.21470.3111.55730.02570.8588-20.661545.8093-50.4139
400.64760.6494-1.7321.6889-2.25324.97110.1452-0.275-0.72541.02791.4221.6598-0.1484-0.0385-1.08980.78350.10960.33092.66020.25581.9794-4.561137.5315-46.2436
414.8714-0.5366-0.59932.01520.10834.4634-0.00060.8522-0.07580.51-0.7130.2596-0.77340.56250.02830.84890.7950.51540.64890.10531.2992-7.897344.1518-53.1621
428.79434.28852.05499.12494.12365.64671.3097-1.1327-0.57810.3202-0.8892-2.48260.85751.118-0.36610.8033-0.1710.11331.74750.48421.0869-11.343840.5639-49.7081
438.5953-1.09830.40194.9890.16325.5297-0.1892-1.02532.2210.44551.07390.7063-0.43151.4614-1.01730.81150.31240.04511.92260.30042.0898-59.630515.5127-5.5611
447.722-3.75064.09042.08131.45357.0847-0.49781.21031.357-0.8462-0.2090.1488-1.12060.58680.5320.0880.77330.19520.82290.34291.2624-62.829111.9984-13.1268
455.8455-2.11630.42159.191-0.24483.7270.50750.2840.9470.0456-0.33150.0236-0.34440.7383-0.03220.72810.29180.05011.08360.09890.8935-72.213710.2903-14.6622
468.5718-2.6722-2.18699.5607-0.71452.0488-1.58361.02880.803-0.5239-1.5137-0.07520.43210.08091.02570.2855-0.50910.27891.37761.6319-0.2308-65.14685.7332-14.6994
470.2985-0.87591.34622.6805-4.20016.45280.15120.4759-0.49661.03-0.19010.63980.2426-0.63160.01980.6214-1.0198-0.1249-0.49620.74371.4547-65.8448-5.1953-8.6229
483.5571-3.0393-0.9327.0704-3.63414.7026-0.371.2696-1.33171.5317-0.34670.1515-0.00761.42240.84630.91910.06130.13071.49160.69571.3305-44.0144-20.3173-0.5923
498.7208-4.4196-2.99791.9842.09982.1284-1.1546-1.4995-1.26330.9091-0.3335-1.0850.3411.24041.55341.4792-0.0150.25851.4430.31171.0533-34.9185-18.403-0.3335
506.65634.76320.40445.86313.41253.795-0.98-0.1947-2.10040.61710.25780.09162.7391-0.70330.71032.2672-0.56080.33482.11160.69251.5465-46.1044-24.5617-2.6293
513.54851.77693.05974.6607-1.21234.9862-0.4666-0.31610.03360.09850.64941.44521.0262-1.0309-0.11611.1568-0.50780.46652.37030.09111.1588-71.7916-15.26735.2056
527.15840.67991.25040.05270.10840.2220.2966-0.54460.0150.17680.6297-0.76330.4198-0.3381-0.23332.10220.91810.92442.71311.530.152-70.6316-18.003319.4026
532.79711.6182-2.33421.1585-0.31425.3088-0.8456-0.6906-0.28581.4693-0.18010.05220.9793-0.43850.47711.53670.80590.27381.4109-0.64930.5327-64.7716-7.322215.5131
540.5328-1.0060.07533.0267-2.47186.72270.6635-0.64520.8825-0.5326-0.71730.340.11071.78110.11371.0218-0.23140.06862.9062-0.33381.0181-51.886-2.0531-0.1305
551.97090.22162.98124.33280.06379.44380.27831.6287-0.0567-0.37340.0233-0.68810.77590.8547-0.16281.1418-0.12590.16452.15690.0840.8314-39.7724-9.0408-21.1193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 203 )
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 222 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 66 )
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 137 )
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 203 )
12X-RAY DIFFRACTION12chain 'B' and (resid 204 through 222 )
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 28 )
14X-RAY DIFFRACTION14chain 'C' and (resid 29 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 81 )
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 106 )
17X-RAY DIFFRACTION17chain 'C' and (resid 107 through 123 )
18X-RAY DIFFRACTION18chain 'C' and (resid 124 through 137 )
19X-RAY DIFFRACTION19chain 'C' and (resid 138 through 171 )
20X-RAY DIFFRACTION20chain 'C' and (resid 172 through 222 )
21X-RAY DIFFRACTION21chain 'D' and (resid 8 through 94 )
22X-RAY DIFFRACTION22chain 'D' and (resid 95 through 137 )
23X-RAY DIFFRACTION23chain 'D' and (resid 138 through 191 )
24X-RAY DIFFRACTION24chain 'D' and (resid 192 through 222 )
25X-RAY DIFFRACTION25chain 'E' and (resid 8 through 50 )
26X-RAY DIFFRACTION26chain 'E' and (resid 51 through 66 )
27X-RAY DIFFRACTION27chain 'E' and (resid 67 through 81 )
28X-RAY DIFFRACTION28chain 'E' and (resid 82 through 137 )
29X-RAY DIFFRACTION29chain 'E' and (resid 138 through 150 )
30X-RAY DIFFRACTION30chain 'E' and (resid 151 through 203 )
31X-RAY DIFFRACTION31chain 'E' and (resid 204 through 222 )
32X-RAY DIFFRACTION32chain 'F' and (resid 8 through 28 )
33X-RAY DIFFRACTION33chain 'F' and (resid 29 through 50 )
34X-RAY DIFFRACTION34chain 'F' and (resid 51 through 66 )
35X-RAY DIFFRACTION35chain 'F' and (resid 67 through 81 )
36X-RAY DIFFRACTION36chain 'F' and (resid 82 through 94 )
37X-RAY DIFFRACTION37chain 'F' and (resid 95 through 106 )
38X-RAY DIFFRACTION38chain 'F' and (resid 107 through 137 )
39X-RAY DIFFRACTION39chain 'F' and (resid 138 through 157 )
40X-RAY DIFFRACTION40chain 'F' and (resid 158 through 171 )
41X-RAY DIFFRACTION41chain 'F' and (resid 172 through 191 )
42X-RAY DIFFRACTION42chain 'F' and (resid 192 through 222 )
43X-RAY DIFFRACTION43chain 'G' and (resid 8 through 66 )
44X-RAY DIFFRACTION44chain 'G' and (resid 67 through 81 )
45X-RAY DIFFRACTION45chain 'G' and (resid 82 through 94 )
46X-RAY DIFFRACTION46chain 'G' and (resid 95 through 106 )
47X-RAY DIFFRACTION47chain 'G' and (resid 107 through 137 )
48X-RAY DIFFRACTION48chain 'G' and (resid 138 through 171 )
49X-RAY DIFFRACTION49chain 'G' and (resid 172 through 203 )
50X-RAY DIFFRACTION50chain 'G' and (resid 204 through 222 )
51X-RAY DIFFRACTION51chain 'H' and (resid 8 through 59 )
52X-RAY DIFFRACTION52chain 'H' and (resid 60 through 72 )
53X-RAY DIFFRACTION53chain 'H' and (resid 73 through 106 )
54X-RAY DIFFRACTION54chain 'H' and (resid 107 through 157 )
55X-RAY DIFFRACTION55chain 'H' and (resid 158 through 222 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more