2F2E

Crystal Structure of PA1607, a Putative Transcription Factor

PDB DOI: https://doi.org/10.2210/pdb2F2E/pdb

Classification: DNA BINDING PROTEIN/STRUCTURAL GENOMICS
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-11-16 Released: 2006-03-14
Deposition Author(s): Sieminska, E.A., Xu, X., Zheng, H., Lunin, V., Cuff, M., Joachimiak, A., Edwards, A., Savchenko, A., Sanders, D.A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.251
R-Value Work: 0.177
R-Value Observed: 0.181

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.

Sieminska, E.A., Xu, X., Savchenko, A., Sanders, D.A.

(2007) Protein Sci 16: 543-549

PubMed: 17322537 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.062668207
Primary Citation of Related Structures:
2F2E

PubMed Abstract:
The structure of the PA1607 protein from Pseudomonas aureginosa was determined at 1.85 A resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. PA1607 forms a dimer and adopts a winged-helix motif similar to the MarR family of transcription regulators, though it has an unusual dimerization profile. The DNA-binding regions and a putative metal-binding site are not conserved in PA1607.

Organizational Affiliation

Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada.

Macromolecule Content

Total Structure Weight: 33.31 kDa
Atom Count: 2,576
Modelled Residue Count: 282
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA1607	A, B	146	Pseudomonas aeruginosa	Mutation(s): 3 Gene Names: PA1607
UniProt
Find proteins for Q9I3B4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I3B4 Go to UniProtKB: Q9I3B4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I3B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [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: 1.85 Å
R-Value Free: 0.251
R-Value Work: 0.177
R-Value Observed: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.884	α = 90
b = 78.865	β = 91.64
c = 78.941	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Advisory, Data collection, Database references, Structure summary