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- PDB-6vhd: FphF, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 6vhd
TitleFphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound
ComponentsEsterase family protein
KeywordsHYDROLASE / FphF / fluorophosphonate-binding / serine hydrolases / sodium bound / acyl / KT129 / intermediate
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
(2~{R})-2-phenylpiperidine-1-carbaldehyde / S-formylglutathione hydrolase / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsFellner, M. / Mace, P.D.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus .
Authors: Fellner, M. / Lentz, C.S. / Jamieson, S.A. / Brewster, J.L. / Chen, L. / Bogyo, M. / Mace, P.D.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase family protein
B: Esterase family protein
C: Esterase family protein
D: Esterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5808
Polymers116,8234
Non-polymers7574
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-31 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.202, 87.202, 455.197
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 55 or resid 57 through 253 or resid 301))
21(chain B and (resid -1 through 55 or resid 57 through 253 or resid 301))
31(chain C and (resid -1 through 55 or resid 57 through 253 or resid 301))
41(chain D and (resid -1 through 55 or resid 57 through 253 or resid 301))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTYRTYR(chain A and (resid -1 through 55 or resid 57 through 253 or resid 301))AA-1 - 551 - 57
12ARGARGASPASP(chain A and (resid -1 through 55 or resid 57 through 253 or resid 301))AA57 - 25359 - 255
136WG6WG6WG6WG(chain A and (resid -1 through 55 or resid 57 through 253 or resid 301))AE301
21GLYGLYTYRTYR(chain B and (resid -1 through 55 or resid 57 through 253 or resid 301))BB-1 - 551 - 57
22ARGARGASPASP(chain B and (resid -1 through 55 or resid 57 through 253 or resid 301))BB57 - 25359 - 255
236WG6WG6WG6WG(chain B and (resid -1 through 55 or resid 57 through 253 or resid 301))BF301
31GLYGLYTYRTYR(chain C and (resid -1 through 55 or resid 57 through 253 or resid 301))CC-1 - 551 - 57
32ARGARGASPASP(chain C and (resid -1 through 55 or resid 57 through 253 or resid 301))CC57 - 25359 - 255
336WG6WG6WG6WG(chain C and (resid -1 through 55 or resid 57 through 253 or resid 301))CG301
41GLYGLYTYRTYR(chain D and (resid -1 through 55 or resid 57 through 253 or resid 301))DD-1 - 551 - 57
42ARGARGASPASP(chain D and (resid -1 through 55 or resid 57 through 253 or resid 301))DD57 - 25359 - 255
436WG6WG6WG6WG(chain D and (resid -1 through 55 or resid 57 through 253 or resid 301))DH301

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Components

#1: Protein
Esterase family protein / Putative esterase / Tributyrin esterase


Mass: 29205.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: EP54_00010, EQ90_02595, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, RK64_00235
Plasmid: M1366 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D6GS23, UniProt: Q2FUY3*PLUS, S-formylglutathione hydrolase
#2: Chemical
ChemComp-6WG / (2~{R})-2-phenylpiperidine-1-carbaldehyde


Mass: 189.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.48 % / Mosaicity: 0.07 °
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 uL ~7.5 mg/ml FphF+KT129 (0.12mM KT129, 12% DMSO, 18 mM HEPES pH 7.5, 8 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.2 M Sodium ...Details: 0.2 uL ~7.5 mg/ml FphF+KT129 (0.12mM KT129, 12% DMSO, 18 mM HEPES pH 7.5, 8 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350. Crystals were soaked for ~20 seconds in 75% reservoir solution and 25% glycerol prior to freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.98→49.28 Å / Num. obs: 73040 / % possible obs: 99.9 % / Redundancy: 27.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.029 / Rrim(I) all: 0.154 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.0224.92.67610729643070.7110.5352.731.598.5
9.7-49.2820.60.0371665180910.0080.03863.199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.29 Å49.28 Å
Translation7.29 Å49.28 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIXdev-3699refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VH9
Resolution: 1.98→49.28 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2131 6711 4.99 %
Rwork0.1761 --
obs0.178 72838 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.92 Å2 / Biso mean: 46.9353 Å2 / Biso min: 20.85 Å2
Refinement stepCycle: final / Resolution: 1.98→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 56 258 8550
Biso mean--55.99 48.31 -
Num. residues----1020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4885X-RAY DIFFRACTION8.434TORSIONAL
12B4885X-RAY DIFFRACTION8.434TORSIONAL
13C4885X-RAY DIFFRACTION8.434TORSIONAL
14D4885X-RAY DIFFRACTION8.434TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-20.33312050.30054055426097
2-2.030.30222530.28243194572100
2.03-2.050.32472160.271441844400100
2.05-2.080.28552350.279843224557100
2.08-2.10.32362330.26141914424100
2.1-2.130.29392360.250143274563100
2.13-2.160.28072190.234542384457100
2.16-2.20.29272140.235442954509100
2.2-2.230.25532370.226342764513100
2.23-2.270.29652100.223142374447100
2.27-2.310.24012160.215842944510100
2.31-2.350.21442150.213542924507100
2.35-2.390.23662190.207442184437100
2.39-2.440.26732210.206643044525100
2.44-2.490.27412450.204342614506100
2.49-2.550.28412190.197242674486100
2.55-2.620.28082220.200742444466100
2.62-2.690.19581960.180542954491100
2.69-2.770.23411910.18242764467100
2.77-2.860.24142260.181243154541100
2.86-2.960.19822270.187842564483100
2.96-3.080.231880.184743104498100
3.08-3.220.19992110.190442944505100
3.22-3.390.22942500.17442234473100
3.39-3.60.16772300.156442794509100
3.6-3.880.17472660.144441984464100
3.88-4.260.19842410.138542574498100
4.27-4.880.17122310.125142724503100
4.88-6.150.17162130.153142814494100
6.15-49.280.18512260.160442694495100
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)
11.14341.33351.82762.54361.88512.21430.0337-0.1363-0.0084-0.19490.1046-0.31210.20020.5455-0.18040.25020.08970.00710.30680.04980.3056-35.120933.7418-11.7352
28.8748-5.77917.03672.0957-9.69239.82570.55990.6476-0.4032-0.9154-0.04320.29061.061-0.0937-0.47820.56310.0007-0.07550.3879-0.0590.3912-43.763422.4596-27.385
31.61980.2405-0.31851.30150.33744.16570.09330.01180.08640.0262-0.1128-0.11990.18510.12570.01960.17790.0374-0.0030.21050.06770.2565-31.525526.8527-7.4674
44.53130.31432.42424.3701-1.19387.5640.3098-0.3898-0.52480.2785-0.12060.10830.6376-0.2157-0.2080.29910.01330.03690.20060.02360.278-34.935417.4788-4.0227
59.13952.4576-1.53288.8293-3.42354.87640.2368-0.7237-0.91890.406-0.5368-1.08090.41761.13750.30840.42420.0337-0.07850.65140.06490.4425-21.908428.031710.5452
65.86974.9473.37722.23948.93899.23580.0415-0.67120.00071.3329-0.16660.57871.1102-0.11570.05570.60580.00510.01280.3780.13030.3862-33.552916.873713.3493
76.8558-0.89010.73163.49440.22895.7484-0.118-0.3205-0.49730.1365-0.0794-0.07220.77130.09610.18110.45060.0491-0.02190.22080.12160.3462-28.259610.6727-0.3425
86.28862.75580.06755.0988-1.21644.05720.1093-0.2578-0.58240.2982-0.1716-0.32790.86040.42790.09080.50390.1429-0.02580.30670.09630.4091-23.58657.19171.939
96.7685.44093.93046.62333.54227.91180.39630.0608-0.71550.3452-0.1819-0.32320.83990.2544-0.22050.42660.15460.0140.28650.04390.3515-25.00613.6686-12.7454
101.56681.0216-0.28915.6556-2.22555.8842-0.05240.28070.1232-0.40970.0508-0.3263-0.39990.34290.00010.20980.02230.0430.38480.02420.3488-16.570549.0926-15.1461
111.9948-0.38880.45141.4892-0.39915.99950.11690.00640.06350.0228-0.0619-0.0222-0.48450.1995-0.06680.1885-0.02350.01680.2199-0.00990.2609-23.597451.9711-4.2099
122.87042.30170.31367.1099-0.07464.20550.2703-0.53150.09210.3118-0.23790.5969-0.2469-0.5061-0.0440.32590.007-0.00250.4552-0.02980.3278-31.032553.75386.2881
132.47113.00430.85327.8282.85517.57550.3668-0.40760.06110.6212-0.35930.1093-0.2887-0.0313-0.02350.2977-0.0190.01770.4196-0.04690.2942-26.363453.720516.474
145.72870.23362.07774.77641.31398.4012-0.0015-0.47040.68860.339-0.04140.0121-1.6053-0.31580.08920.71180.03890.07770.3088-0.0290.4209-31.134566.01016.9544
152.20183.32835.09899.68612.54778.1568-0.3107-0.25020.8804-0.3277-0.11340.4267-1.8415-0.450.59070.77170.11570.10480.4726-0.11410.5407-33.826867.7761.9886
166.96660.461-2.82758.8973-2.48066.02110.45210.05530.94030.0558-0.2888-0.1024-1.2499-0.0484-0.20550.55690.0543-0.02680.31280.0040.3498-30.767263.6993-9.0471
170.62510.5021-1.16782.4185-0.01944.37710.0602-0.0726-0.12370.23330.0936-0.14420.00690.8072-0.16340.21310.04220.00510.44460.00240.3159-13.268843.499-17.2886
181.03290.4219-0.49532.07580.32041.9014-0.02790.22270.0484-0.04620.0635-0.04210.00340.4757-0.04440.19110.07450.03870.56250.04150.3171-13.227137.1757-27.6587
194.70371.47940.41874.0277-0.26022.87490.0370.5852-0.0112-0.27740.0511-0.0804-0.11660.2952-0.11250.26040.15450.04410.7559-0.00060.3305-6.570733.0465-36.5634
209.5618-0.0869-2.09251.1833-0.12572.9988-0.13681.39940.0891-0.37760.12670.19830.2320.16650.04740.48670.0986-0.00110.8375-0.01790.3943-14.026632.8088-48.1532
214.61690.568-2.2031.8150.41974.0054-0.07660.2269-0.1657-0.10550.0784-0.24670.34250.59150.03160.31220.21030.02690.6499-0.00460.3761-4.632923.0059-34.1972
222.20591.48910.77761.2685-0.39742.16430.1952-0.00760.0157-0.1224-0.0134-0.272-0.22260.3118-0.1550.26430.10770.01070.33750.08710.318-35.224936.2987-24.777
230.13890.9832-1.08255.6519-5.07126.3186-0.0037-0.02960.04920.1010.12040.2297-0.026-0.3241-0.12870.2120.0847-0.02830.3835-0.00650.2713-45.121139.2871-19.2195
242.12521.66610.97343.60490.9752.3644-0.04770.05680.20940.0897-0.1080.1375-0.3907-0.38120.13940.3280.1391-0.0450.45040.0710.3478-40.701548.9016-19.1304
250.5132-0.42880.83452.6989-0.88973.26070.02110.29260.0144-0.1639-0.04270.0048-0.1398-0.23070.02060.19980.1004-0.03290.43740.04640.3235-42.023540.7335-34.3833
268.36212.5177-1.54535.41782.83572.5150.03820.03850.0693-0.4204-0.0854-0.0589-0.2123-0.31410.0420.29310.1716-0.07230.37180.10420.3358-47.829449.1397-36.2281
277.1831.66746.18677.35482.63356.2572-0.55740.86520.7109-0.61020.46910.1834-1.04060.56050.06130.54620.01820.02060.73320.12280.4874-29.520952.3641-44.9948
282.12942.0504-2.52446.5107-1.37897.0743-0.03851.163-0.0921-0.5404-0.2093-0.4082-0.02290.58460.29820.51250.2004-0.07840.68750.03710.3835-44.342748.8958-50.6608
292.28891.21320.17064.83270.21563.49880.0180.06980.0113-0.2588-0.06940.1614-0.4186-0.32410.07120.38710.1804-0.08450.44540.11290.3513-49.226255.2674-36.9205
302.06619.43485.72068.94376.02436.5311-0.25650.49040.3248-0.39010.15850.2259-0.849-0.33120.17440.6390.30330.00020.60630.1180.4727-50.16361.3427-43.259
316.3126-0.57835.64230.2422-0.5475.5325-0.316-0.06240.4134-0.01050.03120.2607-1.4171-0.5050.41890.56220.2947-0.04380.59560.04920.4489-48.604261.294-33.3747
326.00481.107-0.65545.9004-0.45264.9061-0.09780.35880.66380.14180.25980.7757-0.7407-0.9426-0.18450.4120.2185-0.05240.45280.07030.3504-47.032155.3539-23.9113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 40 )A25 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 105 )A41 - 105
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 149 )A106 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 167 )A150 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 189 )A168 - 189
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 207 )A190 - 207
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 235 )A208 - 235
9X-RAY DIFFRACTION9chain 'A' and (resid 236 through 253 )A236 - 253
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 40 )B-1 - 40
11X-RAY DIFFRACTION11chain 'B' and (resid 41 through 133 )B41 - 133
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 162 )B134 - 162
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 189 )B163 - 189
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 220 )B190 - 220
15X-RAY DIFFRACTION15chain 'B' and (resid 221 through 235 )B221 - 235
16X-RAY DIFFRACTION16chain 'B' and (resid 236 through 253 )B236 - 253
17X-RAY DIFFRACTION17chain 'C' and (resid -1 through 40 )C-1 - 40
18X-RAY DIFFRACTION18chain 'C' and (resid 41 through 121 )C41 - 121
19X-RAY DIFFRACTION19chain 'C' and (resid 122 through 149 )C122 - 149
20X-RAY DIFFRACTION20chain 'C' and (resid 150 through 189 )C150 - 189
21X-RAY DIFFRACTION21chain 'C' and (resid 190 through 253 )C190 - 253
22X-RAY DIFFRACTION22chain 'D' and (resid -1 through 24 )D-1 - 24
23X-RAY DIFFRACTION23chain 'D' and (resid 25 through 53 )D25 - 53
24X-RAY DIFFRACTION24chain 'D' and (resid 54 through 74 )D54 - 74
25X-RAY DIFFRACTION25chain 'D' and (resid 75 through 133 )D75 - 133
26X-RAY DIFFRACTION26chain 'D' and (resid 134 through 149 )D134 - 149
27X-RAY DIFFRACTION27chain 'D' and (resid 150 through 167 )D150 - 167
28X-RAY DIFFRACTION28chain 'D' and (resid 168 through 189 )D168 - 189
29X-RAY DIFFRACTION29chain 'D' and (resid 190 through 207 )D190 - 207
30X-RAY DIFFRACTION30chain 'D' and (resid 208 through 221 )D208 - 221
31X-RAY DIFFRACTION31chain 'D' and (resid 222 through 235 )D222 - 235
32X-RAY DIFFRACTION32chain 'D' and (resid 236 through 253 )D236 - 253

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