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- PDB-9wxs: Silver-bound E.coli Malate dehydrogenase (C251S) -

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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 / 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 / cytoplasm / cytosol
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

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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)129,8408
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

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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, 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.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 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

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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

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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

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