3F6W | pdb_00003f6w

XRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000

PDB DOI: https://doi.org/10.2210/pdb3F6W/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pseudomonas syringae pv. tomato str. DC3000
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-06 Released: 2008-12-02
Deposition Author(s): Petrova, T., Cuff, M., Shackleford, G., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.248 (Depositor), 0.246 (DCC)
R-Value Work:
0.191 (Depositor), 0.188 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3F6W

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

Literature

XRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000

Petrova, T., Cuff, M., Shackleford, G., Gu, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 46.65 kDa
Atom Count: 4,209
Modeled Residue Count: 408
Deposited Residue Count: 415
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XRE-family like protein	A, B, C, D, E	83	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: PSPTO0717, PSPTO_0717
UniProt
Find proteins for Q889N2 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q889N2 Go to UniProtKB: Q889N2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q889N2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E	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: 0.248 (Depositor), 0.246 (DCC)
R-Value Work: 0.191 (Depositor), 0.188 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.196	α = 90
b = 48.306	β = 98
c = 111.424	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	model building
ARP/wARP	model building
CCP4	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-12-02

Deposition Author(s):

Shackleford, G.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-12-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2023-12-27
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: 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.