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- PDB-6hxo: Structure of the citryl-CoA lyase core module of Chlorobium limic... -

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Basic information

Entry
Database: PDB / ID: 6hxo
TitleStructure of the citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase (space group P21)
ComponentsATP-citrate lyase alpha-subunit
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


acyltransferase activity, acyl groups converted into alkyl on transfer / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / lipid metabolic process / lyase activity / ATP binding / cytoplasm
Similarity search - Function
ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRATE ANION / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-citrate lyase alpha-subunit
B: ATP-citrate lyase alpha-subunit
C: ATP-citrate lyase alpha-subunit
D: ATP-citrate lyase alpha-subunit
E: ATP-citrate lyase alpha-subunit
F: ATP-citrate lyase alpha-subunit
G: ATP-citrate lyase alpha-subunit
H: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,76317
Polymers246,0438
Non-polymers1,7209
Water23,1311284
1
A: ATP-citrate lyase alpha-subunit
C: ATP-citrate lyase alpha-subunit
E: ATP-citrate lyase alpha-subunit
G: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,17410
Polymers123,0214
Non-polymers1,1536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29920 Å2
ΔGint-193 kcal/mol
Surface area33960 Å2
MethodPISA
2
B: ATP-citrate lyase alpha-subunit
D: ATP-citrate lyase alpha-subunit
F: ATP-citrate lyase alpha-subunit
H: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5897
Polymers123,0214
Non-polymers5673
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30560 Å2
ΔGint-191 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.261, 106.416, 105.051
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATP-citrate lyase alpha-subunit


Mass: 30755.354 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Prior to crystallization, the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin digestion.
Source: (gene. exp.) Chlorobium limicola (bacteria) / Gene: aclA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AJC4
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% PEG Smear Broad 0.1 M MES pH 6.5 Protein sample buffer 20 mM HEPES, pH 7.4, 150 mM NaCL supplemented with 50 mM citrate pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 332084 / % possible obs: 97.4 % / Redundancy: 3.47 % / Biso Wilson estimate: 21.52 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.095 / Net I/σ(I): 9.07
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 52538 / CC1/2: 0.324 / Rrim(I) all: 1.641 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of C. limicola ACL holoenzyme

Resolution: 1.5→48.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.211 16515 4.97 %RANDOM
Rwork0.194 ---
obs0.195 332071 97.6 %-
Displacement parametersBiso mean: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.4385 Å20 Å2-0.4348 Å2
2--0.0265 Å20 Å2
3----1.4651 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.5→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15342 0 114 1281 16737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115873HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9521522HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5517SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes366HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2311HARMONIC5
X-RAY DIFFRACTIONt_it15873HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2065SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20494SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 1234 5.2 %
Rwork0.221 22501 -
all0.222 23735 -
obs--94.85 %
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)
10.8510.04840.20760.53990.07310.35890.07570.1609-0.1405-0.0365-0.0442-0.06960.06660.1112-0.0314-0.0420.02310.0161-0.0236-0.0207-0.038734.953944.1343113.3759
25.1101-1.18050.33931.7983-0.05081.58070.1287-0.5156-0.23230.2974-0.0525-0.22910.11250.209-0.07620.0171-0.0418-0.0840.04070.05380.014244.341137.1821137.9409
32.04970.19640.33780.72670.17510.36020.1376-0.1659-0.44670.1418-0.0591-0.13160.16940.0272-0.0785-0.0181-0.0046-0.0263-0.0850.03850.009333.120133.358129.6841
40.4520.36061.00541.17281.60661.87580.1154-0.43830.10060.129-0.30240.27860.0304-0.65280.1870.0282-0.06080.1040.1408-0.1083-0.018713.523662.4481142.1903
50.5575-0.04570.03470.5926-0.01460.622-0.00580.07080.0653-0.0948-0.0340.1087-0.0268-0.09530.0398-0.03170.0040.0039-0.03010.0031-0.043571.359532.955116.2064
60.7348-0.4923-0.40630.80410.42671.0629-0.0315-0.04680.04620.0502-0.02090.1367-0.0587-0.07560.0524-0.0020.01030.0145-0.0178-0.02740.005770.2943.0789139.1271
70.4023-0.0765-0.26470.40810.34150.5474-0.02-0.05140.08110.0216-0.02750.0681-0.0835-0.02170.0475-0.02020.01160.0226-0.0438-0.0187-0.042674.433239.8341132.148
80.18620.4088-0.05761.8162-0.63941.21750.054-0.1857-0.09590.2697-0.1796-0.19740.09340.4140.1256-0.00060.08460.01230.03540.065-0.050193.519311.6223141.9942
90.67450.18920.22940.52310.14541.2555-0.0362-0.15320.16780.1138-0.07810.0877-0.0844-0.15990.1143-0.01680.00260.0234-0.0323-0.0294-0.02727.794770.7006136.2859
103.5147-2.0252.45172.6131-1.50272.57590.32820.49750.1197-0.296-0.4368-0.12920.32120.59630.10850.03810.0562-0.01680.020.0144-0.126151.677372.5849141.7825
111.0337-0.36291.28420.6932-0.59574.4461-0.0117-0.02660.20620.0378-0.0439-0.0457-0.0480.05870.0556-0.0397-0.02390.0106-0.06130.0039-0.019932.662870.8198127.4178
121.1851-0.53030.02762.0290.97450.75490.0680.324-0.0242-0.1486-0.0871-0.1702-0.01230.16930.0191-0.00740.02440.05280.07870.0155-0.028442.42753.7177103.9183
130.3485-0.00010.0490.55-0.2660.6475-0.0652-0.0524-0.07890.0031-0.00390.04460.16850.00060.06910.02640.01580.0631-0.0480.0117-0.048378.53544.8047136.7766
141.788-0.2611-1.47521.93021.40633.0470.01140.08620.15180.20840.11790.2647-0.1088-0.1689-0.12930.09750.10120.1852-0.03750.10620.038258.046110.909146.6642
151.2710.1873-1.50842.71960.07174.07580.13160.34060.0495-0.18960.12270.6942-0.33-0.9688-0.2543-0.10180.06560.03090.06840.09920.010652.26651.9976143.1372
160.25580.1007-0.51250.3017-0.85732.02880.01870.0131-0.0887-0.05310.09970.1498-0.0356-0.2415-0.11840.01-0.01290.0505-0.02590.0171-0.011766.69634.4864134.131
171.0716-1.03850.24582.5766-0.59060.77780.08840.2057-0.0182-0.3564-0.11460.23370.1239-0.1670.02620.0114-0.0095-0.04450.01060.0084-0.034562.745124.6556106.4281
182.8874-0.97460.716401.86291.6627-0.05070.30550.0891-0.11130.0667-0.163-0.01090.5101-0.01590.00310.00520.07540.01730.0767-0.004644.24372.6065105.3057
190.38470.32-0.5631.05571.41684.0268-0.12460.04270.31250.0934-0.0552-0.0848-0.3180.32790.17970.0427-0.0493-0.0804-0.05120.05740.038940.113484.7141126.1087
200.56810.28960.27871.0801-0.01670.5758-0.0464-0.09920.17980.1121-0.06240.1083-0.0961-0.11730.1088-0.00580.00350.0132-0.0307-0.0291-0.003224.507472.1044131.6357
21-0.1733-2.46312.07223.3076-0.73331.049-0.1789-0.05880.0897-0.2954-0.26050.2267-0.0679-0.26880.43940.04710.0226-0.07580.0459-0.06250.121112.174170.2541121.9999
222.4048-0.84354.33291.16380.81556.82610.0651-0.15020.0199-0.2821-0.1166-0.0336-0.1958-0.14660.05150.01770.0684-0.1363-0.1284-0.04390.140215.089482.0577123.7177
231.1439-0.27950.463.2898-1.86382.36210.0841-0.05880.17340.0763-0.05410.1985-0.0535-0.0539-0.03-0.0544-0.01060.0251-0.0586-0.0306-0.042124.440967.4144132.9766
24-0.1643-0.14380.17871.40680.94382.00380.0467-0.27-0.16470.2792-0.0436-0.05010.19-0.3071-0.00310.0325-0.06770.01360.03380.0328-0.054119.916346.0459140.5019
253.40450.0359-0.48591.010.44361.68310.09250.1744-0.7023-0.0325-0.0768-0.00890.2291-0.0919-0.0157-0.0115-0.0383-0.0347-0.0573-0.04650.129512.728730.1849121.2598
260.2163-0.0981-0.22930.709-0.28690.8412-0.06930.0092-0.1029-0.14720.00070.0950.2892-0.0640.06860.0656-0.02070.0561-0.0753-0.0073-0.049775.49841.33127.3456
270.9345-0.5806-1.75110.67030.64876.5160.3124-0.12430.1442-0.09450.24-0.1308-0.79260.6042-0.55230.0728-0.02640.2043-0.0435-0.04530.044799.9314-3.5987124.3078
280.60590.0625-0.0981.0191-0.15420.5568-0.0239-0.03830.03710.0732-0.0083-0.03470.00660.09130.0322-0.04270.00540.0251-0.01790.0147-0.069587.229823.5342133.0067
292.9654-0.6659-0.49520.83710.82520.77110.084-0.1581-0.33110.1535-0.09590.12250.20190.0250.0119-0.0147-0.03790.0084-0.0530.01880.019314.299936.3333126.7833
300.66790.0680.17310.50230.12920.44620.07370.1442-0.1639-0.0346-0.0401-0.01510.08140.0536-0.0336-0.00070.01560.0065-0.0149-0.02370.000228.320742.7508113.043
312.90271.30422.22211.27561.0331.4117-0.0693-0.08110.1369-0.1063-0.09870.2268-0.1941-0.09220.168-0.01790.0249-0.0073-0.0204-0.02420.009316.885256.0113102.4213
328.18440.5956-0.6590.3084-0.08071.46170.00360.5580.4086-0.3282-0.0540.0918-0.0671-0.20530.05050.03630.0563-0.0893-0.03130.08770.073611.806962.496891.9395
331.16730.20180.38210.4330.16990.41190.02970.18770.0031-0.1449-0.0480.0283-0.0150.08420.0183-0.0060.03370.0116-0.028-0.0147-0.054725.968950.04899.88
340.2749-0.29670.51132.901-0.01690.5803-0.03430.16750.19560.0552-0.182-0.2186-0.15490.1440.2163-0.0031-0.0415-0.012-0.01660.0680.037743.461276.9382118.6981
351.7142-0.026-0.18940.3164-0.25640.6557-0.0078-0.13820.11280.08450.0311-0.1506-0.1190.0751-0.0233-0.0343-0.02690.0093-0.012-0.0113-0.019493.269938.8578128.3656
360.74760.59680.31850.585-0.58980.7752-0.03430.110.2321-0.003-0.01870.0227-0.20430.07090.0530.0091-0.0260.0352-0.04510.0261-0.007386.379244.4958117.2034
373.13251.06040.28531.80470.36960.7180.00120.13380.1717-0.2411-0.0361-0.1088-0.10270.10080.03490.06560.00160.0129-0.00190.04310.006180.830340.8044106.6948
380.5837-0.17910.08730.3052-0.29270.22210.00930.02470.0009-0.0741-0.01140.13990.0407-0.08540.00210.0002-0.02360.0072-0.0151-0.0113-0.025368.972322.32118.8955
393.19460.6409-1.99030.7133-0.17612.0805-0.09840.0243-0.0035-0.10930.0073-0.07260.13560.18580.09120.00740.01370.0369-0.00760.0154-0.04988.037421.8077103.5123
409.1761.15811.220201.66923.2350.06190.393-0.6109-0.45110.0368-0.1078-0.18140.3457-0.09870.02270.02320.09070.0835-0.07990.02392.460115.79492.5809
411.19560.4971-0.38222.445-0.41530.96540.02570.28190.024-0.2443-0.0992-0.0044-0.1403-0.03660.07350.03070.014-0.0181-0.03390.0269-0.134878.061129.619496.9054
421.726-0.1052-0.09481.12540.52832.03740.00650.3318-0.0461-0.2561-0.06170.0613-0.018-0.03820.05520.08130.00850.02380.0330.0193-0.055783.993726.315596.4179
432.26940.2264-0.72690.727-0.04210.9753-0.04690.08280.0498-0.13570.0010.06760.0045-0.04380.0459-0.0425-0.0052-0.0019-0.0616-0.0022-0.077673.490628.5483116.2092
440.1842-0.1292-0.4422.459-0.09180.6426-0.00580.1051-0.1786-0.2028-0.07280.31540.2687-0.22280.07870.0987-0.0991-0.0203-0.0136-0.03380.06161.40831.055119.2874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|348 - A|445 }
2X-RAY DIFFRACTION2{ A|446 - A|482 }
3X-RAY DIFFRACTION3{ A|483 - A|581 }
4X-RAY DIFFRACTION4{ A|582 - A|607 }
5X-RAY DIFFRACTION5{ B|348 - B|445 }
6X-RAY DIFFRACTION6{ B|446 - B|518 }
7X-RAY DIFFRACTION7{ B|519 - B|581 }
8X-RAY DIFFRACTION8{ B|582 - B|607 }
9X-RAY DIFFRACTION9{ C|352 - C|451 }
10X-RAY DIFFRACTION10{ C|452 - C|556 }
11X-RAY DIFFRACTION11{ C|557 - C|581 }
12X-RAY DIFFRACTION12{ C|582 - C|607 }
13X-RAY DIFFRACTION13{ D|351 - D|451 }
14X-RAY DIFFRACTION14{ D|452 - D|467 }
15X-RAY DIFFRACTION15{ D|468 - D|534 }
16X-RAY DIFFRACTION16{ D|535 - D|581 }
17X-RAY DIFFRACTION17{ D|582 - D|607 }
18X-RAY DIFFRACTION18{ E|348 - E|357 }
19X-RAY DIFFRACTION19{ E|358 - E|383 }
20X-RAY DIFFRACTION20{ E|384 - E|445 }
21X-RAY DIFFRACTION21{ E|446 - E|543 }
22X-RAY DIFFRACTION22{ E|544 - E|556 }
23X-RAY DIFFRACTION23{ E|557 - E|581 }
24X-RAY DIFFRACTION24{ E|582 - E|593 }
25X-RAY DIFFRACTION25{ E|594 - E|607 }
26X-RAY DIFFRACTION26{ F|348 - F|451 }
27X-RAY DIFFRACTION27{ F|452 - F|556 }
28X-RAY DIFFRACTION28{ F|557 - F|607 }
29X-RAY DIFFRACTION29{ G|352 - G|373 }
30X-RAY DIFFRACTION30{ G|374 - G|445 }
31X-RAY DIFFRACTION31{ G|446 - G|467 }
32X-RAY DIFFRACTION32{ G|468 - G|482 }
33X-RAY DIFFRACTION33{ G|483 - G|581 }
34X-RAY DIFFRACTION34{ G|582 - G|607 }
35X-RAY DIFFRACTION35{ H|352 - H|373 }
36X-RAY DIFFRACTION36{ H|374 - H|398 }
37X-RAY DIFFRACTION37{ H|399 - H|411 }
38X-RAY DIFFRACTION38{ H|412 - H|445 }
39X-RAY DIFFRACTION39{ H|446 - H|467 }
40X-RAY DIFFRACTION40{ H|468 - H|482 }
41X-RAY DIFFRACTION41{ H|483 - H|518 }
42X-RAY DIFFRACTION42{ H|519 - H|556 }
43X-RAY DIFFRACTION43{ H|557 - H|581 }
44X-RAY DIFFRACTION44{ H|582 - H|607 }

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