4WJI | pdb_00004wji

Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP and tyrosine

• PDB DOI: https://doi.org/10.2210/pdb4WJI/pdb

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


• Deposited: 2014-09-30 Released: 2014-10-22 
• Deposition Author(s): Shabalin, I.G., Cooper, D.R., Hou, J., Zimmerman, M.D., Stead, M., Hillerich, B.S., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Literature

Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP

Shabalin, I.G., Cooper, D.R., Hou, J., Zimmerman, M.D., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,522 
• Modeled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase	A	293	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: tyrC EC: 1.3.1 (PDB Primary Data), 1.3.1.12 (UniProt)
UniProt
Find proteins for Q92MG1 (Rhizobium meliloti (strain 1021)) Explore Q92MG1  Go to UniProtKB:  Q92MG1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
TYR	C [auth A]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.40 Å
• R-Value Free:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3BS33

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.409	α = 90
b = 68.891	β = 94.34
c = 51.097	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Shabalin, I.G., Cooper, D.R., Hou, J., Zimmerman, M.D., Stead, M., Hillerich, B.S., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54-GM094662

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Data collection
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary