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- PDB-7cgc: Silver-bound E. coli Malate dehydrogenase (C113 and C251) -

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Basic information

Entry
Database: PDB / ID: 7cgc
TitleSilver-bound E. coli Malate dehydrogenase (C113 and C251)
ComponentsMalate dehydrogenase
KeywordsMETAL BINDING PROTEIN / Malate dehydrogenase / silver
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-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: 2.548 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: 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
DepositionJul 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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)131,19520
Polymers129,4694
Non-polymers1,72616
Water25214
1
A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7995
Polymers32,3671
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-12 kcal/mol
Surface area12760 Å2
MethodPISA
2
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7995
Polymers32,3671
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-13 kcal/mol
Surface area12860 Å2
MethodPISA
3
C: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7995
Polymers32,3671
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area12610 Å2
MethodPISA
4
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7995
Polymers32,3671
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-12 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.222, 125.129, 85.195
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: 32367.191 Da / Num. of mol.: 4 / Mutation: E307Q
Source method: isolated from a genetically manipulated source
Details: Silver bound at C251 and C113 / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: mdh, b3236, JW3205 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61889, malate dehydrogenase
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Tris-HNO3 0.1M pH 7.2, PEG3000 30% / PH range: 7.0-7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2017 / Details: Direct
RadiationMonochromator: 0.97914 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.548→81.43 Å / Num. obs: 37363 / % possible obs: 98 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.34 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.091 / Rrim(I) all: 0.214 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.55-2.616.30.51927740.8250.240.57399.5
11.4-81.435.50.0964470.9850.0430.10699.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.6data scaling
PDB_EXTRACT3.25data extraction
xia20.3.7data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z3W

5z3w


Resolution: 2.548→40.714 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 31.49
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. 3 macro cycles of phenix.refine
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1799 4.82 %Random
Rwork0.2427 ---
obs0.245 37323 97.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.98 Å2 / Biso mean: 35.5243 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 2.548→40.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8698 0 16 14 8728
Biso mean--46.32 31.5 -
Num. residues----1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038801
X-RAY DIFFRACTIONf_angle_d0.49711932
X-RAY DIFFRACTIONf_chiral_restr0.0411465
X-RAY DIFFRACTIONf_plane_restr0.0031547
X-RAY DIFFRACTIONf_dihedral_angle_d2.1795305
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5482-2.61710.42941570.3211271699
2.6171-2.69410.33141260.30752788100
2.6941-2.78110.34811390.2991277299
2.7811-2.88040.30491330.3008274399
2.8804-2.99570.32771410.2898274999
2.9957-3.1320.36121430.2878273999
3.132-3.29710.35111470.2766271198
3.2971-3.50360.27661580.2596267197
3.5036-3.77390.32041260.2467271097
3.7739-4.15330.25181490.2145274298
4.1533-4.75350.25451020.1894262193
4.7535-5.98590.22221450.2108272998
5.9859-40.7140.22891330.1861283399
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)
11.08430.0056-0.53213.06851.64061.13390.03670.1025-0.02830.0767-0.0232-0.30740.1456-0.04720.00870.22110.03790.00380.18720.0180.1848-14.7435-31.679134.1183
23.3014-1.1466-0.17231.86790.11020.3325-0.07220.0613-0.0323-0.0503-0.0460.22060.1332-0.06890.03830.2642-0.02580.0470.2286-0.09170.1883-34.2253-41.0108131.3759
31.4551-1.0738-0.40691.5133-0.1680.54970.00780.2766-0.2469-0.19420.0190.1520.0746-0.10.04820.3064-0.0333-0.00280.28-0.08140.2547-31.2026-43.6043128.909
41.37781.53611.04632.98511.4222.05090.1686-0.27780.12370.172-0.3990.35440.1678-0.40990.2080.2703-0.03750.06640.2156-0.05310.2406-33.0136-25.058390.4969
52.4691-0.70050.92882.4121-0.01341.24980.05840.1739-0.1764-0.0187-0.0637-0.02160.18840.07670.0060.3369-0.02250.02350.2105-0.02420.1594-24.2105-40.662179.1263
61.99831.07540.48012.23260.00813.62360.0430.2434-0.08640.0549-0.0127-0.2065-0.0449-0.1085-0.09710.2606-0.0152-0.00140.1256-0.00610.2492-8.2996-31.395299.6289
72.10661.6130.49961.97370.4682.84020.14350.0833-0.3074-0.0195-0.0314-0.25160.26660.2394-0.18080.27460.0239-0.00990.2275-0.01310.2333-7.1085-35.097101.9983
81.4933-0.53970.76392.3251-0.32871.26380.04930.04410.00380.06580.0699-0.13740.08340.1122-0.12070.2906-0.04130.01690.2199-0.04620.2097-3.3617-20.0632110.3881
92.39910.11791.17552.9850.45111.5061-0.18660.2262-0.0632-0.39980.36030.2164-0.23230.2907-0.02110.3573-0.05560.01650.33490.01940.2147-10.084-4.406101.2101
102.92810.3966-0.35683.4461-0.26852.8487-0.1618-0.10960.5055-0.2204-0.0340.5809-0.2999-0.05720.03130.4034-0.089-0.02630.22550.02460.3409-16.31352.3859102.5671
111.43640.27050.90312.870.23641.11120.28120.28440.3370.1044-0.0352-0.0416-0.21020.1411-0.09290.4145-0.02670.01320.2589-0.05840.2191-13.5096-18.3244101.9778
121.696-0.3733-0.23382.22420.26472.3874-0.11850.4156-0.1083-0.4377-0.0128-0.3624-0.28230.0004-0.09360.2927-0.07710.07240.2389-0.00730.23422.8326-10.6763105.3404
131.1142-0.18790.36372.73450.07560.9181-0.0024-0.05620.05710.04950.1791-0.274-0.0475-0.2065-0.00720.3191-0.09080.04820.1846-0.02140.2576-0.991-6.9802113.103
142.6550.04120.48374.0041.01511.9873-0.1994-0.1919-0.39370.1486-0.26230.16260.0385-0.1930.10120.27080.05990.01890.2258-0.03470.2083-34.9813-16.3653136.1061
151.6620.3226-0.01024.18191.32922.4521-0.14140.21070.194-0.4126-0.02770.3656-0.1649-0.20640.16870.27310.04140.05750.27970.05980.207-39.4234-11.7924130.8029
163.477-1.01780.01283.2444-0.74552.85680.13120.45510.8884-0.0686-0.30720.1651-0.4199-0.29010.12130.30950.04420.01140.23160.04310.3914-36.06171.9245139.0604
173.07-0.93291.46361.3586-0.63321.76130.0001-0.07360.18460.2736-0.00650.0958-0.2112-0.12990.03980.3725-0.03180.02090.12080.00680.2196-25.5819-7.3825152.0881
182.1496-0.28850.41792.0681-0.25432.4979-0.1757-0.12250.19460.16550.0426-0.1513-0.01520.66510.0960.3136-0.06750.01910.30750.00680.3286-13.773-8.5704150.2951
193.1283-1.47310.73432.36380.36722.07110.2495-0.11760.09280.0444-0.14030.2251-0.17440.2311-0.0910.24410.0050.04970.2060.01160.2752-34.0599-13.7605145.6243
202.1931-0.4099-0.24012.0042-0.4642.3598-0.3427-0.27920.08540.65680.22670.09-0.346-0.4032-0.00230.44330.27120.09040.1388-0.01670.3612-35.6822-1.5288152.8758
211.3467-0.72350.71521.143-0.16571.86280.0318-0.49210.71750.5815-0.08690.0311-0.4274-0.17750.16620.61410.1161-0.09370.3184-0.05650.4502-28.95351.2255158.2979
221.543-0.99620.05691.5672-0.88481.9336-0.32270.05520.5402-0.29970.1406-0.1986-0.63330.10950.28560.5188-0.0994-0.07440.16740.08330.6376-27.124711.2829141.6953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 134 )A1 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 188 )A135 - 188
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 311 )A189 - 311
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 134 )B1 - 134
5X-RAY DIFFRACTION5chain 'B' and (resid 135 through 312 )B135 - 312
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 38 )C1 - 38
7X-RAY DIFFRACTION7chain 'C' and (resid 39 through 90 )C39 - 90
8X-RAY DIFFRACTION8chain 'C' and (resid 91 through 162 )C91 - 162
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 188 )C163 - 188
10X-RAY DIFFRACTION10chain 'C' and (resid 189 through 207 )C189 - 207
11X-RAY DIFFRACTION11chain 'C' and (resid 208 through 243 )C208 - 243
12X-RAY DIFFRACTION12chain 'C' and (resid 244 through 271 )C244 - 271
13X-RAY DIFFRACTION13chain 'C' and (resid 272 through 311 )C272 - 311
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 23 )D1 - 23
15X-RAY DIFFRACTION15chain 'D' and (resid 24 through 108 )D24 - 108
16X-RAY DIFFRACTION16chain 'D' and (resid 109 through 134 )D109 - 134
17X-RAY DIFFRACTION17chain 'D' and (resid 135 through 188 )D135 - 188
18X-RAY DIFFRACTION18chain 'D' and (resid 189 through 224 )D189 - 224
19X-RAY DIFFRACTION19chain 'D' and (resid 225 through 242 )D225 - 242
20X-RAY DIFFRACTION20chain 'D' and (resid 243 through 271 )D243 - 271
21X-RAY DIFFRACTION21chain 'D' and (resid 272 through 295 )D272 - 295
22X-RAY DIFFRACTION22chain 'D' and (resid 296 through 311 )D296 - 311

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