3IS6 | pdb_00003is6

The Crystal Structure of a domain of a putative Permease protein from Porphyromonas gingivalis to 2A

• PDB DOI: https://doi.org/10.2210/pdb3IS6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-25 Released: 2009-09-08 
• Deposition Author(s): Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.259 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.213 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

The Crystal Structure of a domain of a putative Permease protein from Porphyromonas gingivalis to 2A

Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.3 kDa 
• Atom Count: 3,664 
• Modeled Residue Count: 454 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative permease protein, ABC transporter	A, B	244	Porphyromonas gingivalis W83	Mutation(s): 0  Gene Names: PG0684, PG_0684
UniProt
Find proteins for Q7MWD8 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MWD8  Go to UniProtKB:  Q7MWD8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.259 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.213 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.39	α = 90
b = 79.193	β = 90
c = 105.086	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary