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- PDB-5z3w: Malate dehydrogenase binds silver at C113 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5z3w
TitleMalate dehydrogenase binds silver at C113
ComponentsMalate dehydrogenase
KeywordsMETAL BINDING PROTEIN / Silver / MDH / inhibition
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity ...malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity / protein homodimerization activity / membrane / cytosol / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SILVER ION / Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsWang, H. / Wang, M. / Sun, H.
Funding support Hong Kong, China, 5items
OrganizationGrant numberCountry
University Grants Committee704612P Hong Kong
University Grants Committee17305415P Hong Kong
University Grants Committee703913P Hong Kong
University Grants Committee1733616P Hong Kong
National Science Foundation (China)21671203 China
CitationJournal: Chem Sci / Year: 2020
Title: Atomic differentiation of silver binding preference in protein targets: Escherichia coli malate dehydrogenase as a paradigm
Authors: Wang, H. / Yang, X. / Wang, M. / Hu, M. / Xu, X. / Yan, A. / Hao, Q. / Li, H. / Sun, H.
History
DepositionJan 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 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: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3848
Polymers128,9524
Non-polymers4314
Water73941
1
A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3462
Polymers32,2381
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-6 kcal/mol
Surface area12550 Å2
MethodPISA
2
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3462
Polymers32,2381
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-6 kcal/mol
Surface area12800 Å2
MethodPISA
3
C: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3462
Polymers32,2381
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-6 kcal/mol
Surface area12690 Å2
MethodPISA
4
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3462
Polymers32,2381
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.648, 124.564, 85.503
Angle α, β, γ (deg.)90.000, 107.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Malate dehydrogenase


Mass: 32238.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: mdh, b3236, JW3205 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61889, malate dehydrogenase
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl 0.1M pH 8.5, MgCl2 0.1M, PEG3350 22% / PH range: 8.0-8.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen flow
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2017
RadiationMonochromator: Graphite Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.29→124.56 Å / Num. obs: 50974 / % possible obs: 87.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.29-2.45.90.16561860.9860.1010.17997.6
7.81-124.566.50.05513510.9970.0230.0699.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12-2829refinement
PDB_EXTRACT3.24data extraction
XDS2017-11data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IB6
Resolution: 2.29→53.565 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.53
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2292 2573 5.05 %
Rwork0.1955 --
obs0.1973 50960 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.99 Å2 / Biso mean: 28.3116 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 2.29→53.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8704 0 4 41 8749
Biso mean--52.36 29.99 -
Num. residues----1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038852
X-RAY DIFFRACTIONf_angle_d0.57612010
X-RAY DIFFRACTIONf_chiral_restr0.0431472
X-RAY DIFFRACTIONf_plane_restr0.0031558
X-RAY DIFFRACTIONf_dihedral_angle_d2.0887300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.33410.27661590.23162671283099
2.3341-2.38170.28541490.22972710285999
2.3817-2.43350.32161160.22832683279998
2.4335-2.49010.30431380.2242624276296
2.4901-2.55240.25981340.21892633276797
2.5524-2.62140.2761210.225527612882100
2.6214-2.69850.23841480.22582708285699
2.6985-2.78560.29351450.21852692283799
2.7856-2.88520.29211640.232527182882100
2.8852-3.00070.26181250.22362729285499
3.0007-3.13720.26681310.21892740287199
3.1372-3.30260.22821400.21392677281798
3.3026-3.50950.24511520.19542676282898
3.5095-3.78040.19081830.18142655283898
3.7804-4.16070.17861510.16742657280897
4.1607-4.76250.18921410.15222559270093
4.7625-5.99890.20061410.18412699284098
5.9989-53.57980.18791350.1562795293099
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)
11.571-0.314-0.54782.4376-1.2561.49730.0611-0.04790.097-0.1549-0.06570.13370.01590.0928-0.02650.1632-0.0295-0.02380.1447-0.00290.134754.230434.140623.8496
20.6260.9249-0.94982.8072-1.73272.0222-0.02650.27690.1226-0.29470.10380.41610.0561-0.3217-0.08980.1635-0.0082-0.03280.15-0.00720.198649.161930.25124.7892
34.15910.75922.04524.44880.5556.30740.0019-0.4858-0.01310.3518-0.07410.4151-0.2349-0.67140.16180.20090.0140.08250.15870.0470.22446.856622.780337.9459
43.51480.97711.20012.7735-0.13634.4311-0.0269-0.1668-0.0543-0.0781-0.10610.00380.02880.0520.15840.1936-0.00340.03870.130.00020.196152.134417.139834.8311
52.43380.05160.02860.4923-0.13010.67640.0024-0.0910.0382-0.0242-0.051-0.12170.0340.16430.05250.1961-0.01710.00770.17360.01790.163166.729419.185731.1613
61.71650.8860.9643.1086-0.77491.9384-0.04250.0894-0.123-0.1774-0.1342-0.38140.08920.19020.12990.17950.02440.05350.28140.08490.346478.104917.516232.1754
72.525-1.7782-1.39015.9571-0.28232.12-0.3191-0.9463-0.06160.72820.4313-0.2148-0.1088-0.0643-0.15840.2789-0.0446-0.04520.47750.01610.240975.72626.953242.0697
82.8682.47492.1956.75784.66734.9314-0.004-0.3166-0.2980.2547-0.0999-0.25050.2885-0.0965-0.00890.1697-0.01230.02130.19380.02320.181863.414624.332924.0561
91.6526-0.19570.53023.1658-1.05477.0656-0.045-0.0066-0.36-0.0879-0.1346-0.20970.12080.38310.18350.12160.01840.05610.15890.01410.290863.369110.732728.3906
104.4623-1.58415.32542.3998-1.62736.46540.62650.7513-0.5103-0.2012-0.4287-0.21350.86050.5549-0.27170.3005-0.02960.01830.282-0.00370.439666.49737.147325.9833
112.3042-0.1766-1.08811.4277-0.07710.98440.2184-0.6407-0.80520.2783-0.2101-0.1192-0.04240.32140.10720.288-0.0121-0.06550.33430.12410.250163.935810.242744.6104
124.8918-1.11190.5344.13440.34232.15390.14060.2698-0.3839-0.1536-0.29350.2682-0.0751-0.1780.0460.0813-0.01380.0090.11330.03830.090486.353236.1005-9.6026
131.0069-1.09721.00331.1889-1.01172.57520.04310.12680.2642-0.0655-0.267-0.2608-0.17060.40550.0360.0973-0.00590.02180.20420.05460.213592.040440.2887-11.83
143.8775-1.229-0.18752.5804-0.56363.13720.16550.0436-0.1426-0.2299-0.5057-0.59940.51990.80310.12890.26590.13510.07810.39780.14680.2405103.784328.1728-8.8125
154.37090.22520.42024.4317-0.55322.08380.0317-0.02190.0485-0.044-0.1952-0.29870.15250.42110.15770.1750.06870.03640.25280.04380.1769100.41526.4245-1.4626
163.07311.3179-0.4330.9291-0.49730.27230.0523-0.2811-0.13620.0988-0.056-0.09930.0991-0.05950.03690.22640.005-0.0070.20620.02550.214785.091822.33971.0468
172.0977-0.56360.49172.0497-1.33323.09270.0611-0.1485-0.2249-0.06510.01980.03720.4362-0.1617-0.04350.3024-0.048-0.00840.1510.0140.221678.153113.4197-1.8138
181.41421.67392.31534.20243.86356.680.2535-0.072-0.06480.35320.11370.11340.4869-0.294-0.3670.1858-0.0065-0.01690.1650.04990.211183.736531.3565-1.4048
191.9598-0.196-0.01536.3366-0.42291.712-0.1034-0.2475-0.17420.45480.16240.42070.0343-0.3038-0.04750.21870.00080.02350.20910.02930.103990.634324.04018.8946
204.83215.00450.03085.8987-0.45120.28730.6114-0.77220.26351.2689-0.70340.2724-0.2141-0.1650.12510.3962-0.0039-0.01550.41360.02830.191988.289923.537213.6031
218.953.8835-2.39012.8005-2.04882.08030.3252-0.1916-0.65450.0043-0.3369-0.43930.32920.24340.14740.37780.1239-0.01540.24560.03310.249196.685710.32812.5243
224.19361.28230.97335.7066-0.54422.8164-0.1735-0.2749-0.1286-0.014-0.1110.02310.23310.07990.21120.1754-0.0047-0.00020.1559-0.01270.085671.393343.092826.6574
230.6492-0.56010.62445.331-0.38751.7621-0.1241-0.05410.01030.27970.1674-0.0959-0.2038-0.1485-0.04430.1304-0.01520.02150.2255-0.01330.168974.516641.455833.0808
241.67610.1513-0.89033.9519-0.4561.45850.1866-0.17210.17050.299-0.157-0.5796-0.0630.2861-0.0130.2048-0.0539-0.01030.3027-0.02660.160176.858547.413531.6933
257.4213-0.4767-0.63873.5488-0.29583.54650.4302-0.95271.16990.3023-0.058-0.0959-0.73310.1364-0.15910.321-0.05130.03520.3557-0.12340.265871.84661.422432.1198
262.68880.96070.60412.20890.48862.61070.0482-0.17640.3259-0.0191-0.00370.0245-0.32270.0763-0.01740.1842-0.00810.03450.1324-0.00730.15468.554556.812518.3726
271.3574-0.1672-0.11692.3614-0.72893.9624-0.07550.03880.0555-0.0537-0.04180.1607-0.2716-0.42640.13460.17630.0068-0.00630.2276-0.01990.249153.83950.949110.1993
288.19252.0878-2.46211.5026-0.78612.2981-0.11340.2590.0601-0.19340.10610.03950.194-0.0391-0.02630.21920.0017-0.00640.17610.01070.205370.585845.777117.3277
295.5377-1.761-0.02335.7205-0.47342.30870.05810.24470.1486-0.51240.06310.3802-0.19870.2685-0.16080.2669-0.0475-0.00340.1682-0.00250.193272.156657.83649.8805
303.89791.19580.62361.0816-0.31741.44140.12120.46310.6108-0.37290.06550.2335-0.11360.1818-0.07170.3721-0.0418-0.07250.19610.02770.293465.535660.45984.3251
313.45430.18223.48941.84570.737.5747-0.62980.05850.85390.0168-0.09570.3079-0.90620.32290.57940.43410.02220.00250.1845-0.05060.508463.434470.820720.7465
321.4634-0.97490.48353.8583-0.40492.2656-0.0086-0.0098-0.1245-0.0244-0.02260.04630.05420.0350.04360.1473-0.0309-0.01040.17-0.00020.159171.158626.5786-17.5357
332.0951-0.59750.08091.2215-0.9753.18360.10120.0424-0.38130.15440.01170.27230.544-0.244-0.11430.18760.0059-0.03810.1572-0.00240.225566.350624.9387-21.5452
342.9027-0.16210.5914.0575-0.85564.9118-0.31690.3372-0.5153-0.8260.07010.12040.6966-0.29650.19930.25570.0111-0.03580.1584-0.05790.189465.194930.4973-35.7545
351.55760.39080.54912.11770.7172.1980.0110.0358-0.0654-0.11420.0639-0.042-0.1083-0.2092-0.0740.12240.03640.00760.14860.00990.125964.964342.2711-26.8139
361.9706-1.75841.66432.2789-1.21911.6658-0.06540.00790.3846-0.0198-0.1059-0.4001-0.2101-0.00370.13640.2156-0.0036-0.00260.1812-0.00360.254777.34154.5967-21.9336
378.67410.7379-2.51781.7488-0.35691.4867-0.2423-0.28440.0082-0.02210.04810.18250.2396-0.09840.12570.1980.0301-0.00880.22060.0090.164867.548339.4765-16.1682
382.65150.5829-0.83153.5559-2.82395.38770.0489-0.0955-0.01630.394-0.0770.0951-0.353-0.38010.03860.13160.02940.00010.1639-0.05630.188758.806248.1918-23.4265
391.19290.39070.67443.1215-0.0430.4320.08570.12950.0743-0.28160.0150.061-0.1309-0.0903-0.08660.17720.032-0.02280.21830.01160.147562.713252.4189-31.8624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 90 )A49 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 108 )A91 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 134 )A109 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 162 )A135 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 195 )A163 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 224 )A196 - 224
8X-RAY DIFFRACTION8chain 'A' and (resid 225 through 242 )A225 - 242
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 271 )A243 - 271
10X-RAY DIFFRACTION10chain 'A' and (resid 272 through 285 )A272 - 285
11X-RAY DIFFRACTION11chain 'A' and (resid 286 through 311 )A286 - 311
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 23 )B1 - 23
13X-RAY DIFFRACTION13chain 'B' and (resid 24 through 90 )B24 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 108 )B91 - 108
15X-RAY DIFFRACTION15chain 'B' and (resid 109 through 135 )B109 - 135
16X-RAY DIFFRACTION16chain 'B' and (resid 136 through 162 )B136 - 162
17X-RAY DIFFRACTION17chain 'B' and (resid 163 through 224 )B163 - 224
18X-RAY DIFFRACTION18chain 'B' and (resid 225 through 242 )B225 - 242
19X-RAY DIFFRACTION19chain 'B' and (resid 243 through 271 )B243 - 271
20X-RAY DIFFRACTION20chain 'B' and (resid 272 through 285 )B272 - 285
21X-RAY DIFFRACTION21chain 'B' and (resid 286 through 311 )B286 - 311
22X-RAY DIFFRACTION22chain 'C' and (resid 1 through 23 )C1 - 23
23X-RAY DIFFRACTION23chain 'C' and (resid 24 through 48 )C24 - 48
24X-RAY DIFFRACTION24chain 'C' and (resid 49 through 90 )C49 - 90
25X-RAY DIFFRACTION25chain 'C' and (resid 91 through 108 )C91 - 108
26X-RAY DIFFRACTION26chain 'C' and (resid 109 through 162 )C109 - 162
27X-RAY DIFFRACTION27chain 'C' and (resid 163 through 224 )C163 - 224
28X-RAY DIFFRACTION28chain 'C' and (resid 225 through 242 )C225 - 242
29X-RAY DIFFRACTION29chain 'C' and (resid 243 through 271 )C243 - 271
30X-RAY DIFFRACTION30chain 'C' and (resid 272 through 295 )C272 - 295
31X-RAY DIFFRACTION31chain 'C' and (resid 296 through 311 )C296 - 311
32X-RAY DIFFRACTION32chain 'D' and (resid 1 through 48 )D1 - 48
33X-RAY DIFFRACTION33chain 'D' and (resid 49 through 90 )D49 - 90
34X-RAY DIFFRACTION34chain 'D' and (resid 91 through 108 )D91 - 108
35X-RAY DIFFRACTION35chain 'D' and (resid 109 through 162 )D109 - 162
36X-RAY DIFFRACTION36chain 'D' and (resid 163 through 224 )D163 - 224
37X-RAY DIFFRACTION37chain 'D' and (resid 225 through 242 )D225 - 242
38X-RAY DIFFRACTION38chain 'D' and (resid 243 through 271 )D243 - 271
39X-RAY DIFFRACTION39chain 'D' and (resid 272 through 311 )D272 - 311

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