2NQW | pdb_00002nqw

Structure of the transporter associated domain from PG_0272, a CBS domain protein from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb2NQW/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-31 Released: 2006-11-28 
• Deposition Author(s): Cuff, M.E., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Structure of the transporter associated domain from PG_0272, a CBS domain protein from Porphyromonas gingivalis.

Cuff, M.E., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.91 kDa 
• Atom Count: 975 
• Modeled Residue Count: 87 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain protein	A	93	Porphyromonas gingivalis W83	Mutation(s): 1  Gene Names: PG_0272
UniProt
Find proteins for Q7MXD1 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXD1  Go to UniProtKB:  Q7MXD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.30 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.733	α = 90
b = 45.195	β = 90
c = 57.214	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Cuff, M.E., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Structure summary