3BY6 | pdb_00003by6

Crystal structure of a transcriptional regulator from Oenococcus oeni

PDB DOI: https://doi.org/10.2210/pdb3BY6/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Oenococcus oeni PSU-1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-01-15 Released: 2008-02-19
Deposition Author(s): Zhang, R., Volkart, L., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.278 (Depositor), 0.281 (DCC)
R-Value Work:
0.239 (Depositor), 0.244 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BY6

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

Literature

The crystal structure of a transcriptional regulator from Oenococcus oeni.

Zhang, R., Volkart, L., Gu, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 69.28 kDa
Atom Count: 4,777
Modeled Residue Count: 602
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted transcriptional regulator	A, B, C, D, E	126	Oenococcus oeni PSU-1	Mutation(s): 0 Gene Names: GI:116491763, OEOE_1803
UniProt
Find proteins for Q04D30 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1)) Explore Q04D30 Go to UniProtKB: Q04D30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04D30
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.278 (Depositor), 0.281 (DCC)
R-Value Work: 0.239 (Depositor), 0.244 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.434	α = 90
b = 103.893	β = 102.85
c = 131.393	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.