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- PDB-5f78: Crystal structure of Mutant N87T of adenosine/Methylthioadenosine... -

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Basic information

Entry
Database: PDB / ID: 5f78
TitleCrystal structure of Mutant N87T of adenosine/Methylthioadenosine phosphorylase from Schistosoma mansoni in APO form
ComponentsMethylthioadenosine phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleus / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8518 Å
AuthorsTorini, J.R.S. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: PLoS Negl Trop Dis / Year: 2016
Title: Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway.
Authors: Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.D.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,05512
Polymers211,4796
Non-polymers5766
Water33,3821853
1
A: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0286
Polymers105,7393
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-102 kcal/mol
Surface area33970 Å2
MethodPISA
2
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0286
Polymers105,7393
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-105 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.193, 82.232, 150.746
Angle α, β, γ (deg.)90.000, 101.550, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTrimer confirmed by gel filtration

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Components

#1: Protein
Methylthioadenosine phosphorylase


Mass: 35246.484 Da / Num. of mol.: 6 / Fragment: Enzyme / Mutation: N87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1853 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5 / PH range: 6.1-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.85→28.05 Å / Num. all: 161035 / Num. obs: 161035 / % possible obs: 97.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.8 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L5Y
Resolution: 1.8518→28.05 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 8062 5.02 %Random selection
Rwork0.1712 152613 --
obs0.1726 160675 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.1 Å2 / Biso mean: 26.6607 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.8518→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13039 0 30 1853 14922
Biso mean--15.15 36.18 -
Num. residues----1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313328
X-RAY DIFFRACTIONf_angle_d0.56118098
X-RAY DIFFRACTIONf_chiral_restr0.0452103
X-RAY DIFFRACTIONf_plane_restr0.0042318
X-RAY DIFFRACTIONf_dihedral_angle_d12.0227990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8518-1.87280.28852490.24275088533797
1.8728-1.89490.24822410.24355125536697
1.8949-1.9180.28332750.24825015529097
1.918-1.94220.27632750.24644981525696
1.9422-1.96780.23682720.21565035530796
1.9678-1.99470.25032550.20954841509693
1.9947-2.02320.20552510.19584816506792
2.0232-2.05340.22112830.18614946522996
2.0534-2.08550.22362840.20295206549099
2.0855-2.11970.20812640.1785118538299
2.1197-2.15620.20712640.17645170543499
2.1562-2.19540.23582880.17765146543499
2.1954-2.23760.20352960.1695123541999
2.2376-2.28330.21342830.1915094537798
2.2833-2.33290.20793250.17485103542899
2.3329-2.38710.21372840.16845131541598
2.3871-2.44680.1952790.16745092537198
2.4468-2.51290.20392750.16325150542598
2.5129-2.58680.2022610.16625065532697
2.5868-2.67020.18952530.16425074532796
2.6702-2.76560.17382510.16095024527596
2.7656-2.87620.20552560.16364768502492
2.8762-3.0070.2132850.17455039532496
3.007-3.16530.20022600.17465227548799
3.1653-3.36330.19882710.162552195490100
3.3633-3.62250.17772700.161252475517100
3.6225-3.98610.1752630.14685262552599
3.9861-4.56080.15522810.13435191547299
4.5608-5.73810.15932160.14874943515992
5.7381-28.05610.19192520.17245374562699
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)
13.6035-1.36551.27243.0192-0.05141.82480.18920.9206-0.3289-0.8815-0.1751-0.53180.38220.8221-0.03840.310.05040.16650.36-0.01910.474142.0697-17.3170.7083
21.9201-1.2957-0.26023.2282-0.02393.769-0.003-0.0342-0.2099-0.1391-0.23970.10560.52320.21210.13460.33550.06670.15480.1309-0.05840.41734.172-29.2152.0838
31.0104-0.64970.1071.0510.42341.0706-0.12850.0917-0.1951-0.23590.0429-0.37530.17560.2640.04860.19480.03290.11770.1711-0.0280.384136.3033-20.20395.2106
41.65060.2037-0.42051.5657-0.17631.8199-0.0453-0.1926-0.1184-0.021-0.0166-0.2589-0.0140.27670.05870.1032-0.01090.02540.1375-0.01050.18934.784-9.21115.8719
52.9470.6022-0.45411.594-0.98461.23370.2439-0.27880.16360.1374-0.2346-0.1831-0.42240.39450.03470.2345-0.08560.05230.1609-0.04820.198935.84153.090811.9655
64.40351.16170.79351.92680.22293.9424-0.0052-0.08480.1022-0.07740.0893-0.2181-0.2722-0.0899-0.06010.1104-0.00990.03890.0732-0.00250.116617.3404-1.499311.0754
71.34340.67850.29081.8386-0.28212.20180.0342-0.0728-0.1298-0.0546-0.0885-0.18460.10430.11670.04950.1037-0.01240.03670.11970.00010.207730.3008-12.695614.9432
83.8982-1.45621.92413.3179-2.69675.0541-0.11730.1021-0.0447-0.02550.45640.4585-0.4918-0.3908-0.36940.2223-0.02230.06230.16360.04050.289828.1887-1.50742.8797
97.6729-3.79143.70513.9221-2.64955.2665-0.07350.82160.0751-0.3159-0.0711-0.3958-0.27590.48790.08210.2579-0.06790.12360.2576-0.0180.334939.6488-4.281-0.8298
104.4530.0276-0.37680.43560.72961.3021-0.2018-0.8714-1.0140.1423-0.1006-0.66050.51830.65940.1920.32070.1389-0.07650.42980.10250.551242.3058-23.850324.9567
110.64171.5135-0.19334.2273-1.62442.5353-0.2215-0.4676-0.58990.0946-0.026-0.49110.28610.270.25010.14540.0294-0.01160.25150.08610.223111.4623-32.233843.4042
122.7476-1.21873.38135.9417-5.41888.12230.1133-0.0641-0.5448-0.20990.07050.11481.0471-0.2067-0.16720.315-0.00910.03660.14690.01430.28738.107-38.556530.64
131.29590.49-0.86941.1328-0.57852.7617-0.0865-0.1423-0.287-0.0392-0.0808-0.11820.29390.12490.17120.147-0.00040.01150.11460.05620.164810.0747-30.387136.1401
142.15850.18780.92450.9666-0.28612.54010.0093-0.0535-0.0154-0.0061-0.0701-0.0657-0.00640.11020.04650.15920.00330.01920.08560.02890.09288.9308-16.721529.6549
151.5334-0.3947-0.17570.43710.03281.83170.15-0.44940.28830.3132-0.0507-0.1649-0.62470.2997-0.03740.341-0.1173-0.01840.2775-0.02060.165813.4229-10.823648.0543
164.7643-1.8996-1.44026.79121.58754.30930.0968-0.11650.14340.2883-0.1497-0.1369-0.150.34620.05780.1233-0.0384-0.00140.14470.03290.100625.3498-9.669926.3877
170.5202-0.22590.21040.6513-0.08920.80440.078-0.1126-0.0236-0.0132-0.1837-0.2997-0.12120.33140.00690.1402-0.0402-0.00230.21520.06870.174117.5496-17.105934.5525
186.1518-0.1189-1.50151.20490.01771.2508-0.1176-0.6814-0.06480.205-0.1306-0.38650.00490.69460.23470.232-0.0553-0.05580.48850.16640.259922.5151-23.510247.6651
191.7133-0.40821.06861.0773-0.79134.53730.0572-0.1427-0.02730.03660.13580.18230.0144-1.0678-0.15160.1214-0.01650.03320.24440.01450.1744-8.0212-20.505135.6116
201.8868-1.16241.93611.68670.16087.02640.18030.0862-0.2276-0.2196-0.00650.43930.3238-0.7218-0.13670.21550.0023-0.03380.1642-0.00760.1826-11.7836-9.16980.2839
210.9733-0.0957-0.12261.6890.28330.7990.04340.06340.0325-0.1052-0.0241-0.0073-0.0729-0.0761-0.01610.12540.00970.00360.08280.00460.0689-0.0717-5.60525.5386
220.67240.0799-0.23080.7222-0.15853.1111-0.0045-0.0627-0.01180.0332-0.0157-0.0931-0.04520.05740.03430.11230.0032-0.00490.06010.00640.10866.0897-6.274316.3361
232.26830.0813-0.62051.7413-0.0041.538-0.0677-0.072-0.0341-0.1396-0.00540.0797-0.00750.00220.05720.18490.0384-0.0010.0642-0.00960.1116-4.3497-2.59176.9742
242.21370.5824-0.03191.8083-0.44471.45760.0126-0.1869-0.18630.1337-0.06090.31290.1375-0.19210.05990.1047-0.02550.02070.12250.0050.185130.019617.681170.2784
251.1929-0.1524-0.2240.84440.11931.22010.01410.11090.0007-0.0993-0.05010.1286-0.0808-0.17420.01940.08710.0269-0.02260.10430.00050.112133.200631.700858.8483
262.5807-0.5945-0.48141.74740.33451.8022-0.0047-0.1709-0.03830.08520.00810.1712-0.0027-0.18090.01340.08570.0208-0.02190.12480.00990.17327.887128.68765.3049
271.308-2.0095-1.38663.24621.6792.8858-0.08110.5662-0.5724-0.1945-0.03710.31760.1434-0.39150.36340.19940.01470.01980.3278-0.15040.22853.55537.788829.4515
280.9594-0.0694-0.67781.15940.63492.6702-0.03820.1396-0.29750.02-0.0419-0.08950.23470.06840.07020.1630.0360.01750.1533-0.070.210855.93588.060437.7196
291.6842-0.17110.24990.87730.50712.21520.10560.29120.0235-0.25-0.0889-0.0671-0.1729-0.0687-0.01020.21720.02850.04320.1476-0.01290.113255.19525.1735.8902
301.1812-0.0425-0.66160.55550.34690.97530.13870.27140.042-0.2466-0.0824-0.0285-0.1815-0.137-0.03930.18470.04390.00430.1627-0.01620.099447.153827.350839.2498
313.68620.6434-1.32530.4798-0.06210.5681-0.1469-0.1970.1539-0.0548-0.05560.2769-0.1483-0.46970.00710.22090.094-0.02010.525-0.15850.243437.953722.217735.6071
320.8959-0.3486-0.72090.73750.36631.2333-0.00840.6987-0.2077-0.6745-0.30580.27030.0561-0.7789-0.12050.29290.1095-0.12980.6199-0.35380.057743.767616.01524.9119
331.04810.11851.10641.24670.10215.23740.02910.21950.041-0.14010.0298-0.4569-0.06341.17330.00730.19120.00920.09850.4106-0.03430.35873.141620.750836.9311
341.4201-0.3624-0.39982.13340.65982.69250.0992-0.5001-0.18190.3258-0.047-0.81840.58490.9912-0.24290.1892-0.0214-0.10290.37240.07490.291176.874931.387571.2298
354.27842.499-1.56021.8022-0.9240.56410.2927-0.8449-0.54130.4615-0.361-0.5891-0.00670.6421-0.00420.22920.0207-0.06230.30480.11820.346470.548219.090474.2765
361.84920.36421.11.60650.42251.71890.0731-0.2744-0.24360.1842-0.1941-0.38870.25860.4915-0.31060.1301-0.0247-0.07560.260.07360.216873.438827.348869.1721
371.5070.30070.95032.41270.77193.31160.1018-0.2458-0.14540.352-0.1073-0.04480.03040.05940.00590.0979-0.0208-0.0160.14220.03360.124866.462829.737172.7693
381.58530.4979-0.43411.0523-0.49021.03410.087-0.03210.0751-0.0121-0.0478-0.0579-0.11260.0946-0.0530.1078-0.0157-0.01970.082-0.00720.108762.168841.099163.5814
390.66070.172-0.34151.0471-0.08314.2784-0.01470.0335-0.0229-0.0989-0.0162-0.0763-0.044-0.03240.04350.0807-0.0112-0.01070.06710.00170.104658.983834.181556.1873
401.97660.03420.55011.5665-0.2120.187-0.01820.5967-0.0389-0.33650.0486-0.11550.2139-0.16670.0530.2222-0.06360.03970.2212-0.02190.145369.99437.126754.3108
413.6553-0.3375-3.19052.80642.3888.0633-0.03740.07640.0389-0.12-0.0661-0.3756-0.02250.28350.01390.111-0.0373-0.01480.1290.06060.197679.283940.287461.112
426.55794.2892.08644.89082.14021.840.4312-0.73230.23310.5588-0.46340.1841-0.0549-0.13530.06160.2555-0.05710.01720.2179-0.0250.103955.919637.105782.3839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 23 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 38 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 90 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 164 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 182 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 198 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 220 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 221 through 238 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 239 through 270 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 271 through 291 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 23 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 24 through 38 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 90 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 139 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 140 through 182 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 183 through 198 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 199 through 238 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 239 through 269 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 270 through 291 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 23 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 24 through 182 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 183 through 220 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 221 through 291 )C0
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 90 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 91 through 220 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 221 through 291 )D0
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 23 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 24 through 90 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 91 through 164 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 165 through 220 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 221 through 240 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 241 through 270 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 271 through 291 )E0
34X-RAY DIFFRACTION34chain 'F' and (resid 3 through 23 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 24 through 38 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 39 through 67 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 68 through 89 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 90 through 182 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 183 through 220 )F0
40X-RAY DIFFRACTION40chain 'F' and (resid 221 through 241 )F0
41X-RAY DIFFRACTION41chain 'F' and (resid 242 through 269 )F0
42X-RAY DIFFRACTION42chain 'F' and (resid 270 through 291 )F0

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