4KTO | pdb_00004kto

Crystal Structure Of a Putative Isovaleryl-CoA dehydrogenase (PSI-NYSGRC-012251) from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb4KTO/pdb

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


• Deposited: 2013-05-20 Released: 2013-06-19 
• Deposition Author(s): Kumar, P.R., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Himmel, D., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Putative Isovaleryl-CoA dehydrogenase from Sinorhizobium meliloti 1021

Kumar, P.R., Hillerich, B., Love, J., Seidel, R., 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: 182.5 kDa 
• Atom Count: 12,031 
• Modeled Residue Count: 1,500 
• Deposited Residue Count: 1,640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isovaleryl-CoA dehydrogenase	A, B, C, D	410	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: ivdH, SM_b21121 EC: 1.3.99.10 (PDB Primary Data), 1.3.8.4 (UniProt)
UniProt
Find proteins for Q92VK1 (Rhizobium meliloti (strain 1021)) Explore Q92VK1  Go to UniProtKB:  Q92VK1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], I [auth C], J [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TRS	F [auth A], H [auth B], K [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.912	α = 90
b = 115.158	β = 90
c = 143.619	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Kumar, P.R., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Himmel, D., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary