1VL0 | pdb_00001vl0

CRYSTAL STRUCTURE OF A DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORTHOLOG (CA_C2315) FROM CLOSTRIDIUM ACETOBUTYLICUM ATCC 824 AT 2.05 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VL0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-06-30 Released: 2004-08-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of DTDP-4-dehydrorhamnose reductase, rfbD ortholog (CAC2315) from Clostridium acetobutylicum at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 101.79 kDa 
• Atom Count: 7,191 
• Modeled Residue Count: 842 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DTDP-4-dehydrorhamnose reductase, rfbD ortholog	A, B, C	292	Clostridium acetobutylicum ATCC 824	Mutation(s): 4  Gene Names: CAC2315 EC: 1.1.1.133
UniProt
Find proteins for Q97GQ1 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97GQ1  Go to UniProtKB:  Q97GQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	D [auth A], F [auth B], G [auth C]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
UNL	E [auth A]	Unknown ligand BOPGDPNILDQYTO-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VL0

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.8	α = 90
b = 130.67	β = 90
c = 151.05	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary