2I6X | pdb_00002i6x

The structure of a predicted HAD-like family hydrolase from Porphyromonas gingivalis.

PDB DOI: https://doi.org/10.2210/pdb2I6X/pdb

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

Deposited: 2006-08-29 Released: 2006-10-10
Deposition Author(s): Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.276 (Depositor), 0.256 (DCC)
R-Value Work:
0.209 (Depositor), 0.203 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2I6X

This is version 1.3 of the entry. See complete history.

Literature

The structure of a predicted HAD-like family hydrolase from Porphyromonas gingivalis. (CASP Target)

Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.61 kDa
Atom Count: 1,845
Modeled Residue Count: 205
Deposited Residue Count: 211
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, haloacid dehalogenase-like family	A	211	Porphyromonas gingivalis W83	Mutation(s): 6 Gene Names: PG_0725
UniProt
Find proteins for Q7MWA6 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MWA6 Go to UniProtKB: Q7MWA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MWA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.276 (Depositor), 0.256 (DCC)
R-Value Work: 0.209 (Depositor), 0.203 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.727	α = 90
b = 78.727	β = 90
c = 139.879	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	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

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Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.