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- PDB-3t0t: Crystal structure of S. aureus Pyruvate Kinase -

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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 / kinase activity / magnesium ion binding / ATP binding
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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


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

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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: 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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