4IPT | pdb_00004ipt

The crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008

• PDB DOI: https://doi.org/10.2210/pdb4IPT/pdb
• Entry: 4IPT supersedes: 3R14

• Classification: LYASE, ISOMERASE
• Organism(s): Veillonella parvula DSM 2008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-10 Released: 2013-02-06 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The crystal structure of a short-chain dehydrogenases/reductase (ethylated) from Veillonella parvula DSM 2008

Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.64 kDa 
• Atom Count: 1,940 
• Modeled Residue Count: 218 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase	A	221	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0111

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A], G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ELY	A	L-PEPTIDE LINKING	C10 H22 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.681	α = 90
b = 60.758	β = 90
c = 68.769	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3R14

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary