[English] 日本語
Yorodumi
- PDB-9wxs: Silver-bound E.coli Malate dehydrogenase (C251S) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wxs
TitleSilver-bound E.coli Malate dehydrogenase (C251S)
ComponentsMalate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / Dehydrogenase
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / 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 / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / 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-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 domain superfamily
Similarity search - Domain/homology
SILVER ION / Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWang, H. / Wang, M. / Sun, H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17307017 Hong Kong
CitationJournal: Chem Sci / Year: 2025
Title: Unprecedented allosteric inhibition of E. coli malate dehydrogenase by silver(i) from atomic resolution analysis.
Authors: Wang, H. / Wang, M. / Yang, X. / Yan, A. / Hao, Q. / Li, H. / Sun, H.
History
DepositionSep 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8408
Polymers129,4084
Non-polymers4314
Water10,683593
1
A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,3521
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area12770 Å2
MethodPISA
2
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,3521
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area12700 Å2
MethodPISA
3
C: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,3521
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area12890 Å2
MethodPISA
4
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,3521
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 156.280, 77.390
Angle α, β, γ (deg.)90.000, 109.200, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Malate dehydrogenase


Mass: 32352.113 Da / Num. of mol.: 4 / Mutation: C251S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mdh, b3236, JW3205 / Variant: C251S / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61889, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#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.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 % / Description: Cuboid-like transparent crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Tris-HCl pH 7.2, 20% PEG 3350 / PH range: 5.5-6.5 / Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.56→36.543 Å / Num. obs: 159361 / % possible obs: 97.5 % / Redundancy: 6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.102 / Rrim(I) all: 0.243 / Net I/σ(I): 8.5
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
1.56-1.66.91.16480424115920.670.4881.264296.3
6.98-36.545.80.0871077018510.9930.0390.09622.998.6

-
Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.16_3549:000refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KKA

5kka


Resolution: 1.56→36.543 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.74
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2965 7965 5 %
Rwork0.266 --
obs0.2675 159164 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.23 Å2 / Biso mean: 25.5639 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.56→36.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 4 593 9327
Biso mean--22.81 30.36 -
Num. residues----1205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.56-1.57770.44222880.3969489696
1.5777-1.59630.43952570.3837497396
1.5963-1.61580.43262650.3723504396
1.6158-1.63620.39142700.3494487196
1.6362-1.65770.37472980.3436502496
1.6577-1.68040.40162260.336500596
1.6804-1.70450.37522670.3238495696
1.7045-1.72990.3622830.3069498397
1.7299-1.75690.34272910.3063495496
1.7569-1.78570.35232740.3136500497
1.7857-1.81650.35862670.2957496297
1.8165-1.84960.35092620.2961507297
1.8496-1.88510.3172710.2814495797
1.8851-1.92360.35732690.2752502397
1.9236-1.96540.32272700.2693503597
1.9654-2.01110.30962100.2765509397
2.0111-2.06140.33642630.2723505697
2.0614-2.11720.31492800.2758500897
2.1172-2.17950.32032860.2766502897
2.1795-2.24980.28932530.2821507697
2.2498-2.33020.34322550.2797506098
2.3302-2.42350.35272410.2959512798
2.4235-2.53370.33332580.3022504798
2.5337-2.66730.32232600.3032511998
2.6673-2.83430.37222470.2993511698
2.8343-3.05310.30792830.3128509398
3.0531-3.36010.29932730.2764511799
3.3601-3.84590.23182420.2087515399
3.8459-4.84360.18363100.1807511698
4.8436-36.5430.19362460.1873523299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01660.0709-0.02460.0447-0.01940.0036-0.00540.04350.0414-0.0159-0.01820.01760.0825-0.112-00.1614-0.0069-0.00740.1573-0.00030.177212.83412.3896-5.3622
2-0.0017-0.0130.01730.0471-0.0090.00220.0144-0.0728-0.1597-0.19220.10830.0173-0.1316-0.20480.00070.2076-0.0185-0.01210.2483-0.00230.17837.449519.04863.0508
30.165-0.07130.16770.0646-0.10710.15590.07980.0408-0.0851-0.0142-0.03960.06510.0744-0.37020.02110.17730.02230.01720.2444-0.0220.16766.994724.41649.2051
40.0982-0.25460.20820.0471-0.04190.10960.021-0.03390.00450.0437-0.04670.01050.0663-0.0025-00.1898-0.00510.00950.232-0.00990.191321.758210.220315.9974
5-0.0095-0.01780.0230.04410.03630.0645-0.0554-0.09690.0813-0.1322-0.08250.1543-0.08680.0424-0.00040.207-0.0424-0.03650.28070.02190.193937.626815.121416.3268
6-0.01380.03330.02480.0361-0.0730.0212-0.0251-0.01530.02520.0402-0.0498-0.0654-0.0199-0.1501-0.00010.1768-0.0383-0.00760.23250.00930.195721.496710.25885.291
70.07380.00350.10760.168-0.07440.13470.0175-0.2116-0.0277-0.0273-0.01570.0169-0.0386-0.0833-0.00130.1752-0.01450.00430.247-0.01730.190917.266910.319223.2436
80.00770.0147-0.07680.0581-0.01940.1194-0.0024-0.03980.0198-0.0114-0.0577-0.0046-0.01170.1751-00.1472-0.00040.00540.14720.00720.157435.041511.8396-5.286
9-0.01340.00490.01550.0458-0.02450.06220.12950.0004-0.01490.042-0.09670.0064-0.0660.24790.00010.16720.0082-0.00010.2342-0.01110.184442.435512.1289-5.6189
100.00860.0320.05840.18220.11230.0812-0.0559-0.107-0.1-0.04470.04110.0192-0.0760.1707-0.00120.17090.00450.0250.2317-0.00610.170738.873315.4289-22.8127
110.03020.0206-0.0141-0.04050.0120.0114-0.00280.05330.0207-0.02730.0152-0.00760.0367-0.03140.00150.1579-0.00340.0150.16960.00190.161925.66814.6474-22.8263
120.03360.03460.0343-0.0006-0.03050.0803-0.03020.1209-0.0543-0.0298-0.0094-0.02640.02440.1039-0.0020.19020.02180.00910.1016-0.00260.161417.4650.5034-22.1645
130.03830.0843-0.16830.1005-0.03640.4123-0.0370.06080.0207-0.03720.0322-0.0130.0064-0.0133-00.19040.0056-0.01760.157-0.0060.164618.4216.9572-22.5366
140.07-0.07170.01450.0447-0.00660.02080.05390.083-0.0872-0.0620.0312-0.04010.1384-0.04710.00020.23080.0229-0.00120.17720.00790.197532.514-0.1682-28.4747
150.0371-0.0182-0.00560.0262-0.06960.0968-0.0767-0.056-0.03570.0095-0.0539-0.00180.08190.0674-0.00690.25750.0209-0.02140.1779-0.02080.221931.6505-5.0309-29.1341
160.1074-0.0255-0.01690.11490.09690.0518-0.06160.2685-0.0269-0.15510.0455-0.0303-0.1377-0.0310.00920.2248-0.03180.03180.20240.00120.136527.927411.7006-37.5478
170.0232-0.03360.05720.0402-0.07080.0603-0.03030.0254-0.02870.04780.02520.02890.01070.002400.1567-0.002-0.00130.1772-0.00420.16683.8329-24.68229.0843
18-0.0307-0.05660.03360.07190.07640.17860.0853-0.13370.0333-0.0538-0.10190.0195-0.0787-0.27750.00130.1584-0.0023-0.00640.2127-0.0060.1828-4.766-30.2276-2.4334
190.0844-0.1104-0.0293-0.1416-0.03540.2253-0.0607-0.02240.0238-0.01920.01880.0241-0.0050.03-00.1513-0.01360.00130.1611-0.00940.180714.9557-28.0578-12.925
200.09740.15580.02160.04540.00460.0723-0.00910.0790.0029-0.0123-0.0027-0.0083-0.02580.0228-0.00010.1749-0.00380.0020.1786-0.00940.172810.814-26.4653-14.2111
210.02190.142-0.07750.14760.09340.2223-0.00710.01350.032-0.00280.1049-0.00460.1730.21510.00160.20590.0448-0.00260.1934-0.02340.182525.5958-37.178313.6984
22-0.08410.1021-0.0848-0.02740.44780.3206-0.0438-0.04870.04450.10630.0668-0.0360.01040.1345-0.00270.19750.0215-0.00440.1356-0.0110.168317.9818-25.071130.4448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 91 )A59 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 108 )A92 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 195 )A109 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 216 )A196 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 242 )A217 - 242
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 311 )A243 - 311
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 48 )B1 - 48
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 71 )B49 - 71
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 135 )B72 - 135
11X-RAY DIFFRACTION11chain 'B' and (resid 136 through 162 )B136 - 162
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 178 )B163 - 178
13X-RAY DIFFRACTION13chain 'B' and (resid 179 through 243 )B179 - 243
14X-RAY DIFFRACTION14chain 'B' and (resid 244 through 271 )B244 - 271
15X-RAY DIFFRACTION15chain 'B' and (resid 272 through 285 )B272 - 285
16X-RAY DIFFRACTION16chain 'B' and (resid 286 through 311 )B286 - 311
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 58 )C1 - 58
18X-RAY DIFFRACTION18chain 'C' and (resid 59 through 108 )C59 - 108
19X-RAY DIFFRACTION19chain 'C' and (resid 109 through 207 )C109 - 207
20X-RAY DIFFRACTION20chain 'C' and (resid 208 through 311 )C208 - 311
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 108 )D1 - 108
22X-RAY DIFFRACTION22chain 'D' and (resid 109 through 311 )D109 - 311

+
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