3IUO | pdb_00003iuo

The Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A

PDB DOI: https://doi.org/10.2210/pdb3IUO/pdb

Classification: HYDROLASE
Organism(s): Porphyromonas gingivalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-08-31 Released: 2009-09-08
Deposition Author(s): Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.221 (Depositor), 0.253 (DCC)
R-Value Work:
0.188 (Depositor), 0.227 (DCC)
R-Value Observed:
0.190 (Depositor)

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

Literature

The Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A

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

To be published.

Macromolecule Content

Total Structure Weight: 29.12 kDa
Atom Count: 1,999
Modeled Residue Count: 221
Deposited Residue Count: 244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase RecQ	A, B	122	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: PG0684, PG_0416, recQ-1 EC: 5.6.2.4
UniProt
Find proteins for Q7MX11 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MX11 Go to UniProtKB: Q7MX11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MX11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 1.60 Å
R-Value Free: 0.221 (Depositor), 0.253 (DCC)
R-Value Work: 0.188 (Depositor), 0.227 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.326	α = 90
b = 98.326	β = 90
c = 72.526	γ = 120

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

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Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-06
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.