3F0C | pdb_00003f0c

Crystal structure of transcriptional regulator from Cytophaga hutchinsonii ATCC 33406

PDB DOI: https://doi.org/10.2210/pdb3F0C/pdb

Classification: transcription regulator
Organism(s): Cytophaga hutchinsonii ATCC 33406
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-24 Released: 2008-11-11
Deposition Author(s): Nocek, B., Maltseva, N., Tan, K., Abdullah, J., Eschenfeldt, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.271 (Depositor), 0.294 (DCC)
R-Value Work:
0.209 (Depositor), 0.234 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3F0C

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

Literature

Crystal structure of transcriptional regulator from Cytophaga hutchinsonii ATCC 33406

Nocek, B., Maltseva, N., Tan, K., Abdullah, J., Stols, L., Eschenfeldt, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 25.71 kDa
Atom Count: 1,546
Modeled Residue Count: 193
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A	216	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: ycdC, CHU_0940

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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: 2.96 Å
R-Value Free: 0.271 (Depositor), 0.294 (DCC)
R-Value Work: 0.209 (Depositor), 0.234 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.099	α = 90
b = 116.099	β = 90
c = 46.367	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
Coot	model building
MLPHARE	phasing
DM	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-11

Deposition Author(s):

Eschenfeldt, W.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-11-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-10-09
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.