5Z3W | pdb_00005z3w

Malate dehydrogenase binds silver at C113

• PDB DOI: https://doi.org/10.2210/pdb5Z3W/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2018-01-09 Released: 2019-01-16 
• Deposition Author(s): Wang, H., Wang, M., Sun, H.
• Funding Organization(s): University Grants Committee, National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Atomic differentiation of silver binding preference in protein targets: Escherichia coli malate dehydrogenase as a paradigm

Wang, H., Yang, X., Wang, M., Hu, M., Xu, X., Yan, A., Hao, Q., Li, H., Sun, H.

(2020) Chem Sci 

• DOI: https://doi.org/10.1039/D0SC04151C

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 129.38 kDa 
• Atom Count: 8,785 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D	311	Escherichia coli K-12	Mutation(s): 1  Gene Names: mdh, b3236, JW3205 EC: 1.1.1.37
UniProt
Find proteins for P61889 (Escherichia coli (strain K12)) Explore P61889  Go to UniProtKB:  P61889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG	E [auth A], F [auth B], G [auth C], H [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.648	α = 90
b = 124.564	β = 107.1
c = 85.503	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Wang, H., Wang, M., Sun, H.

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Funding Organization	Location	Grant Number
University Grants Committee	Hong Kong	704612P
University Grants Committee	Hong Kong	17305415P
University Grants Committee	Hong Kong	703913P
University Grants Committee	Hong Kong	1733616P
National Science Foundation (China)	China	21671203

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description