[English] 日本語
Yorodumi
- PDB-3t0t: Crystal structure of S. aureus Pyruvate Kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t0t
TitleCrystal structure of S. aureus Pyruvate Kinase
ComponentsPyruvate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tetramer / ligand / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphohistidine domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel ...Phosphohistidine domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-I30 / PHOSPHATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsWorrall, L.J. / Vuckovic, M. / Strynadka, N.C.J.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Cheminformatics-driven discovery of selective, nanomolar inhibitors for staphylococcal pyruvate kinase.
Authors: Axerio-Cilies, P. / See, R.H. / Zoraghi, R. / Worral, L. / Lian, T. / Stoynov, N. / Jiang, J. / Kaur, S. / Jackson, L. / Gong, H. / Swayze, R. / Amandoron, E. / Kumar, N.S. / Moreau, A. / ...Authors: Axerio-Cilies, P. / See, R.H. / Zoraghi, R. / Worral, L. / Lian, T. / Stoynov, N. / Jiang, J. / Kaur, S. / Jackson, L. / Gong, H. / Swayze, R. / Amandoron, E. / Kumar, N.S. / Moreau, A. / Hsing, M. / Strynadka, N.C. / McMaster, W.R. / Finlay, B.B. / Foster, L.J. / Young, R.N. / Reiner, N.E. / Cherkasov, A.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,20910
Polymers262,0834
Non-polymers1,1266
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-82 kcal/mol
Surface area89450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.090, 113.090, 315.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 10000
2111B1 - 10000
3111C1 - 10000
4111D1 - 10000

-
Components

#1: Protein
Pyruvate kinase / / PK


Mass: 65520.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: pyk, SAR1776 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GG09, pyruvate kinase
#2: Chemical ChemComp-I30 / N'-[(1E)-1-(1H-benzimidazol-2-yl)ethylidene]-5-bromo-2-hydroxybenzohydrazide


Mass: 373.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13BrN4O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 8.5
Details: 15-20% PEG3350, 0.4 M sodium malonate, 0.1 M bicine, pH 8.5, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.91839 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 14, 2010 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91839 Å / Relative weight: 1
ReflectionResolution: 3.1→113.12 Å / Num. all: 64847 / Num. obs: 64847 / % possible obs: 90.6 % / Redundancy: 6 % / Rsym value: 0.128 / Net I/σ(I): 8.3
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.275.90.75005384301.12380.9
3.27-3.475.91.14777081360.68882.5
3.47-3.715.71.94516578770.3985.1
3.71-45.53.14242777140.23889.6
4-4.385.44.64040574860.15694.3
4.38-4.95.56.13889070260.11597.5
4.9-5.666.15.33844563300.12699.6
5.66-6.936.95.13683053580.12599.8
6.93-9.87.812.23256141730.049100
9.8-56.568.214.91889623170.03899.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→113.09 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.1893 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8399 / SU B: 43.235 / SU ML: 0.326 / SU Rfree: 0.3972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 3283 5.1 %RANDOM
Rwork0.2037 ---
obs0.2048 64727 90.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 217.04 Å2 / Biso mean: 92.3929 Å2 / Biso min: 42.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.07 Å2-0 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 3.1→113.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17628 0 66 0 17694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02217874
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211950
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.98224182
X-RAY DIFFRACTIONr_angle_other_deg0.88329554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25452328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71525.856724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.986153352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.32315100
X-RAY DIFFRACTIONr_chiral_restr0.0680.22928
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219738
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023028
Refine LS restraints NCS

Ens-ID: 1 / Number: 7390 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.020.05
2BTIGHT POSITIONAL0.020.05
3CTIGHT POSITIONAL0.020.05
4DTIGHT POSITIONAL0.020.05
1ATIGHT THERMAL4.220.5
2BTIGHT THERMAL4.850.5
3CTIGHT THERMAL4.390.5
4DTIGHT THERMAL5.20.5
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 217 -
Rwork0.337 4051 -
all-4268 -
obs--80.56 %
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)
12.9466-0.3807-0.30394.95860.70282.2385-0.06930.37280.4012-0.50690.3708-0.9216-0.28520.4001-0.30150.5567-0.10150.01480.4710.03580.531353.91531.867-24.772
211.5350.51010.66237.5772-1.74536.5430.1179-0.4420.37790.4815-0.0292-0.7653-0.71390.0707-0.08880.82420.049-0.22380.2710.01930.586441.84756.111-5.626
31.2437-2.1082-0.214612.27769.797110.610.0013-0.07690.1436-0.61740.0964-0.0249-0.4912-0.447-0.09770.6406-0.1412-0.00710.53580.31540.617539.92142.28-22.878
45.4061-1.1991-1.16424.64041.43777.4273-0.21640.47450.299-0.55940.05050.5124-0.4804-0.56130.1660.4496-0.0402-0.13020.18280.17410.425834.98132.01-22.538
55.66910.87651.12822.94810.82274.1626-0.1424-0.41010.43470.28720.2646-0.4142-0.3420.3872-0.12220.5172-0.0118-0.08920.18640.00370.382947.91925.797-9.127
65.0093.43940.46474.14460.49752.49760.2103-0.2085-0.00750.3564-0.0307-0.50430.02690.3544-0.17960.34430.0487-0.06520.1846-0.06870.300243.2239.279-14.454
78.09723.8438-2.60017.2349-2.803911.2919-0.32930.9138-0.0248-0.61430.583-0.40480.0370.4765-0.25380.3426-0.0635-0.03050.2281-0.04420.296140.39310.981-28.174
813.2745-1.2247-2.27926.73461.620910.28980.06491.1120.2842-0.60330.029-0.29560.19920.0991-0.0940.4232-0.12480.01910.1957-0.0820.243738.0840.122-30.132
94.7427-1.40912.751911.9591-1.10461.83530.0654-0.5574-0.93120.15670.1185-1.82950.2416-0.0073-0.18390.83250.11080.12040.89990.20871.159349.816-31.342-20.307
105.26833.57261.442312.19610.46424.02870.1172-0.3323-0.8783-0.2795-0.4739-0.9838-0.18670.09760.35670.62190.19940.01180.67550.04260.741245.186-28.494-22.746
114.13010.44230.29643.39180.10783.89620.1095-0.0423-0.5776-0.13190.0760.43710.5759-0.3602-0.18550.4268-0.0587-0.04620.257-0.04630.18994.504-35.457-21.388
129.4207-3.1407-1.5937.770.56926.2004-0.3338-1.1433-1.06190.89030.38441.02770.7084-0.6825-0.05061.09340.01390.08030.76760.36560.779214.247-55.6083.06
132.9394-1.88031.54366.015-9.782929.0392-0.0349-0.2901-0.58090.12370.26180.17370.36950.644-0.22680.5715-0.0045-0.12390.17980.02660.299618.143-45.088-16.067
147.619-0.851.89724.42910.364910.92660.0652-0.0502-0.2239-0.085-0.1346-0.3015-0.05350.5110.06940.27640.0378-0.08280.0818-0.04760.159123.052-34.846-17.051
157.58241.9894-1.21052.2822-0.43053.720.0287-1.0528-0.38960.50410.06860.01640.5281-0.0994-0.09740.50110.0668-0.04530.2935-0.0070.18178.682-26.559-6.54
163.73193.1611-1.36924.203-0.78251.35150.0358-0.1130.37280.28220.04470.2821-0.1494-0.1393-0.08040.31030.0833-0.06610.189-0.05920.13914.007-11.191-14.22
177.91693.6640.84516.02120.60285.539-0.36080.71190.0203-0.80710.3721-0.1568-0.2529-0.2333-0.01140.31720.0355-0.03230.1145-0.02620.148718.379-15.277-26.989
188.271-1.43462.26866.4444-0.828211.86470.07641.02-0.2307-0.4186-0.02010.4501-0.05010.2278-0.05630.3431-0.0956-0.11890.1612-0.00080.178620.943-4.92-30.613
199.4626-8.6686-1.941913.6855-1.65223.8459-0.21580.26621.25670.72150.70591.1091-0.921-0.9404-0.49010.9810.0919-0.33540.8440.11341.83328.27127.592-28.035
205.55043.69690.458610.7303-2.35284.471-0.18370.56431.1721-0.15240.22131.4648-0.4365-0.3408-0.03770.71770.1091-0.28970.67910.20861.087813.13824.433-29.376
212.18960.6393-0.96253.7664-0.53063.32450.361-0.5039-0.6890.4308-0.04490.7320.5342-0.4428-0.3160.515-0.2921-0.05160.62220.10.7205-8.114-21.86721.851
229.3133-0.2956-1.093710.23831.03693.53270.00750.6458-0.8454-0.8786-0.38571.28750.392-0.24930.37810.5394-0.0432-0.22771.1249-0.20540.9727-28.302-13.988-3.256
234.8464-1.67218.07063.62481.371719.13420.11490.0191-0.2775-0.0407-0.18250.40110.2365-0.24030.06770.2533-0.22350.15020.82130.00670.5287-17.827-8.69115.554
245.3795-1.68890.14584.5158-0.125813.34790.0508-0.36130.1480.1359-0.12890.5412-0.4124-0.54360.07820.0451-0.04950.06980.32-0.12950.2929-7.609-3.66816.194
252.5045-0.206-0.03725.13290.50744.45790.31120.2209-0.4246-0.472-0.20320.30470.6612-0.2617-0.10790.2766-0.00290.00070.4084-0.11880.34290.798-18.6966.744
265.21243.99150.88945.33592.281.83520.1259-0.0009-0.5533-0.1883-0.0335-0.26320.27340.1828-0.09240.42090.105-0.09290.3417-0.08880.178716.12-12.74614.039
278.98195.44980.3637.2807-2.83166.10650.0604-0.78420.05690.6114-0.33220.12580.8452-0.34260.27190.5343-0.0630.08880.3855-0.06320.181111.957-7.49926.453
288.9648-2.7962.23856.8107-1.72168.8256-0.2313-0.7258-0.49110.68280.3780.30890.2527-0.4096-0.14670.1714-0.06830.02570.4548-0.09310.100822.293-4.62629.912
2914.4406-2.40751.84927.25130.30340.62080.42020.3715-1.4493-0.0858-0.3298-1.9340.27640.5223-0.09040.78760.22510.00951.0850.26031.163454.891-17.28928.271
3012.27953.0284-0.39368.1917-0.82295.62310.1535-0.1294-0.99960.0989-0.5044-1.09260.26520.32010.3510.55440.1951-0.1130.65130.0830.61851.706-12.35529.256
314.056-0.0521-0.04133.21790.29171.94910.1296-0.40740.68930.32820.0268-0.4111-0.25270.3369-0.15630.3087-0.1621-0.03780.5773-0.06460.307159.30627.65921.876
327.43850.22532.23478.11222.02647.9330.00320.64280.6451-0.6030.0235-0.5332-0.33350.3055-0.02670.32220.03730.17660.80040.05360.692883.41514.3913.379
3310.0455-3.0668-4.77372.21931.47692.34390.0506-0.4365-0.3607-0.0269-0.162-0.81110.13960.15060.11140.4006-0.0941-0.07020.7070.00410.771169.64813.53720.746
342.4396-1.7718-1.32865.51050.31239.13270.0769-0.454-0.44810.4934-0.3667-0.40760.54960.48030.28980.1451-0.0659-0.08860.52880.06860.357459.3588.62120.748
352.48080.7181-0.31256.4673-2.1594.6355-0.12220.27240.1354-0.88110.1033-0.4576-0.21380.66050.01890.1978-0.08080.02820.5523-0.07320.271253.14520.7786.637
363.4952.7113-0.0962.6224-1.12642.5826-0.15870.20510.2786-0.22730.12680.1125-0.09370.02310.03190.24090.01560.09170.3349-0.06530.232636.63416.46612.303
376.06161.0929-3.15633.57021.5153.13140.2011-0.57650.1250.0061-0.1409-0.1621-0.27740.0218-0.06020.18620.133-0.0440.4593-0.11560.182738.37914.43726.149
387.3247-2.8399-1.39956.16242.57288.6174-0.1691-0.16980.45440.70550.046-0.50560.17250.07860.12310.1115-0.0901-0.02850.3631-0.07510.142527.50512.27828.292
3910.73970.53692.13452.3639-0.86533.1648-0.31930.24231.5809-0.23910.12411.1272-0.5943-0.82190.19530.55440.1341-0.07630.722-0.13130.8904-3.94923.52117.879
4011.68914.4211-0.65798.1744-0.09774.7475-0.1562-0.41661.0347-0.1664-0.1931.0197-0.123-0.08270.34930.32590.146-0.00880.5722-0.1620.5865-1.11119.03120.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 85
2X-RAY DIFFRACTION2A86 - 155
3X-RAY DIFFRACTION3A156 - 183
4X-RAY DIFFRACTION4A184 - 240
5X-RAY DIFFRACTION5A241 - 317
6X-RAY DIFFRACTION6A318 - 379
7X-RAY DIFFRACTION7A380 - 427
8X-RAY DIFFRACTION8A428 - 470
9X-RAY DIFFRACTION9A471 - 523
10X-RAY DIFFRACTION10A524 - 583
11X-RAY DIFFRACTION11B1 - 85
12X-RAY DIFFRACTION12B86 - 155
13X-RAY DIFFRACTION13B156 - 183
14X-RAY DIFFRACTION14B184 - 240
15X-RAY DIFFRACTION15B241 - 317
16X-RAY DIFFRACTION16B318 - 379
17X-RAY DIFFRACTION17B380 - 427
18X-RAY DIFFRACTION18B428 - 470
19X-RAY DIFFRACTION19B471 - 523
20X-RAY DIFFRACTION20B524 - 583
21X-RAY DIFFRACTION21C1 - 85
22X-RAY DIFFRACTION22C86 - 155
23X-RAY DIFFRACTION23C156 - 183
24X-RAY DIFFRACTION24C184 - 240
25X-RAY DIFFRACTION25C241 - 317
26X-RAY DIFFRACTION26C318 - 379
27X-RAY DIFFRACTION27C380 - 427
28X-RAY DIFFRACTION28C428 - 470
29X-RAY DIFFRACTION29C471 - 523
30X-RAY DIFFRACTION30C524 - 583
31X-RAY DIFFRACTION31D1 - 85
32X-RAY DIFFRACTION32D86 - 155
33X-RAY DIFFRACTION33D156 - 183
34X-RAY DIFFRACTION34D184 - 240
35X-RAY DIFFRACTION35D241 - 317
36X-RAY DIFFRACTION36D318 - 379
37X-RAY DIFFRACTION37D380 - 427
38X-RAY DIFFRACTION38D428 - 470
39X-RAY DIFFRACTION39D471 - 523
40X-RAY DIFFRACTION40D524 - 583

+
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