2NR7 | pdb_00002nr7

Structural Genomics, the crystal structure of putative secretion activator protein from Porphyromonas gingivalis W83

• PDB DOI: https://doi.org/10.2210/pdb2NR7/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-11-01 Released: 2006-12-05 
• Deposition Author(s): Tan, K., Bigelow, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

The crystal structure of putative secretion activator protein from Porphyromonas gingivalis W83

Tan, K., Bigelow, L., Gu, M., 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: 22.28 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 194 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secretion activator protein, putative	A	195	Porphyromonas gingivalis W83	Mutation(s): 1
UniProt
Find proteins for Q7MXB3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXB3  Go to UniProtKB:  Q7MXB3

Small Molecules

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:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.537	α = 90
b = 36.386	β = 119.75
c = 62.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Tan, K., Bigelow, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-12-05
  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: 2024-10-30
  Changes: Structure summary