2P3P

Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83

PDB DOI: https://doi.org/10.2210/pdb2P3P/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-03-09 Released: 2007-04-10
Deposition Author(s): Nocek, B., Hatzos, C., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.226
R-Value Work: 0.165
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of a domain of an uncharacterized protein PG_1388 from Porphyromonas gingivalis W83

Nocek, B., Hatzos, C., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 47.63 kDa
Atom Count: 3,863
Modelled Residue Count: 395
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	207	Porphyromonas gingivalis W83	Mutation(s): 4 Gene Names: PG_1388
UniProt
Find proteins for Q7MUU3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MUU3 Go to UniProtKB: Q7MUU3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MUU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.226
R-Value Work: 0.165
R-Value Observed: 0.168
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.753	α = 86.55
b = 48.259	β = 79.58
c = 54.191	γ = 68.35

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.