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)

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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) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

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

Revision History  

• 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