3EH7 | pdb_00003eh7

The structure of a putative 4-hydroxybutyrate CoA-transferase from Porphyromonas gingivalis W83

• PDB DOI: https://doi.org/10.2210/pdb3EH7/pdb

• Classification: TRANSFERASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-11 Released: 2008-12-09 
• Deposition Author(s): Cuff, M.E., Duggan, E., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

The structure of a putative 4-hydroxybutyrate CoA-transferase from Porphyromonas gingivalis W83

Cuff, M.E., Duggan, E., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.41 kDa 
• Atom Count: 3,362 
• Modeled Residue Count: 401 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybutyrate CoA-transferase	A	434	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: abfT-1, PG_0690
UniProt
Find proteins for Q7MWD3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MWD3  Go to UniProtKB:  Q7MWD3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.704	α = 90
b = 72.704	β = 90
c = 133.694	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Cuff, M.E., Duggan, E., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary