2NVV | pdb_00002nvv

Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16.

• PDB DOI: https://doi.org/10.2210/pdb2NVV/pdb

• Classification: HYDROLASE
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-13 Released: 2007-01-30 
• Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Yong, W., Ho, C.K., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.287 (Depositor), 0.306 (DCC) 
• R-Value Observed: 
  0.287 (Depositor) 

Literature

Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16

Forouhar, F., Neely, H., Seetharaman, J., Yong, W., Ho, C.K., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 338.94 kDa 
• Atom Count: 23,178 
• Modeled Residue Count: 2,976 
• Deposited Residue Count: 3,036 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA hydrolase/transferase family protein	A, B, C, D, E, F	506	Porphyromonas gingivalis W83	Mutation(s): 13  Gene Names: PG1013
UniProt
Find proteins for Q7MVN7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVN7  Go to UniProtKB:  Q7MVN7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.287 (Depositor), 0.306 (DCC) 
• R-Value Observed: 0.287 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.051	α = 90
b = 131.051	β = 90
c = 162.093	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Yong, W., Ho, C.K., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Structure summary