1Y9Q | pdb_00001y9q

Crystal Structure of HTH_3 family Transcriptional Regulator from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb1Y9Q/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-16 Released: 2005-01-04 
• Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal Structure of HTH_3 family Transcriptional Regulator from Vibrio cholerae

Kumaran, D., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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.

Macromolecule Content 

• Total Structure Weight: 22.18 kDa 
• Atom Count: 1,542 
• Modeled Residue Count: 178 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator, HTH_3 family	A	192	Vibrio cholerae	Mutation(s): 5
UniProt
Find proteins for Q9KQN0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQN0  Go to UniProtKB:  Q9KQN0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MED	C [auth A]	D-METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-SCSAIBSYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.226	α = 90
b = 79.226	β = 90
c = 49.849	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary