3R6D | pdb_00003r6d

Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine

• PDB DOI: https://doi.org/10.2210/pdb3R6D/pdb

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


• Deposited: 2011-03-21 Released: 2011-04-20 
• Deposition Author(s): Chang, C., 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: 1.25 Å
• R-Value Free: 
  0.179 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine

Chang, C., 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 kDa 
• Atom Count: 2,291 
• Modelled Residue Count: 221 
• 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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.179 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.446	α = 90
b = 60.721	β = 90
c = 69.612	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Chang, C., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary