3KV1 | pdb_00003kv1

Crystal Structure of Putative Sugar-Binding Domain of Transcriptional Repressor from Vibrio fischeri

• PDB DOI: https://doi.org/10.2210/pdb3KV1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-28 Released: 2009-12-22 
• Deposition Author(s): Kim, Y., Marshall, N., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.165 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal Structure of Putative Sugar-Binding Domain of Transcriptional Repressor from Vibrio fischeri

Kim, Y., Marshall, N., Bearden, J., 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: 29.87 kDa 
• Atom Count: 2,330 
• Modeled Residue Count: 253 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor	A	267	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: lsrR, VF_A0400 EC: 2.7.1.69
UniProt
Find proteins for Q5E0H6 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E0H6  Go to UniProtKB:  Q5E0H6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.70 Å
• R-Value Free:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.165 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.382	α = 90
b = 43.474	β = 104.15
c = 47.536	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Kim, Y., Marshall, N., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary