1Y9Q

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 ?
R-Value Free: 0.224
R-Value Work: 0.199
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KQN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MED Query on MED Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	D-METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-SCSAIBSYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.90 ?
R-Value Free: 0.224
R-Value Work: 0.199
R-Value Observed: 0.199
Space Group: P 3₁ 2 1

Unit Cell:

Length ( ? )	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

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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 (Full details and data files)

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

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1Y9Q

Crystal Structure of HTH_3 family Transcriptional Regulator from Vibrio cholerae

Crystal Structure of HTH_3 family Transcriptional Regulator from Vibrio cholerae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)