3L0D

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bartonella henselae with bound NAD

• PDB DOI: https://doi.org/10.2210/pdb3L0D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bartonella henselae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-09 Released: 2009-12-29 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bartonella henselae with bound NAD

Edwards, T.E., Abendroth, J., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.34 kDa 
• Atom Count: 5,126 
• Modelled Residue Count: 664 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase	A, B	356	Bartonella henselae	Mutation(s): 0  Gene Names: gap, BH15080 EC: 1.2.1.12
UniProt
Find proteins for Q8L201 (Bartonella henselae) Explore Q8L201  Go to UniProtKB:  Q8L201

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M33L0D

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.776	α = 90
b = 91.776	β = 90
c = 161.402	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description