4EJM | pdb_00004ejm

Crystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021 bound to NADP

• PDB DOI: https://doi.org/10.2210/pdb4EJM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-06 Released: 2012-05-02 
• Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of a putative zinc-binding dehydrogenase (target nysgrc-012003) from sinorhizobium meliloti 1021 bound to NADP

Sampathkumar, P., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Fiser, A., Gizzi, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Love, J.D., Matikainen, B., Patskovsky, Y., Seidel, R., Toro, R., Zencheck, W., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 40.01 kDa 
• Atom Count: 2,683 
• Modeled Residue Count: 342 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative zinc-binding dehydrogenase	A	370	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R01577, SMc01214 EC: 1.1.1
UniProt
Find proteins for Q92PZ3 (Rhizobium meliloti (strain 1021)) Explore Q92PZ3  Go to UniProtKB:  Q92PZ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.62	α = 90
b = 107.62	β = 90
c = 137.741	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary