8ZF2 | pdb_00008zf2

Quorum Sensing master regulator HapR of Photobacterium marinum

PDB DOI: https://doi.org/10.2210/pdb8ZF2/pdb

Classification: TRANSCRIPTION
Organism(s): Photobacterium marinum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-07 Released: 2025-05-07
Deposition Author(s): Basu Choudhury, G., Saha, A., Datta, S., Ray Chaudhuri, S.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Quorum Sensing master regulator HapR of Photobacterium marinum

Basu Choudhury, G., Saha, A., Datta, S., Ray Chaudhuri, S.

To be published.

Macromolecule Content

Total Structure Weight: 46.66 kDa
Atom Count: 3,503
Modeled Residue Count: 379
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quorum-sensing regulator of virulence HapR	A, B	201	Photobacterium marinum	Mutation(s): 0 Gene Names: C942_04851
UniProt
Find proteins for L8JC63 (Photobacterium marinum) Explore L8JC63 Go to UniProtKB: L8JC63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L8JC63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.6	α = 70.39
b = 44.31	β = 72.78
c = 61.026	γ = 85.11

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM	data scaling
PROTEUM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Basu Choudhury, G.

Ray Chaudhuri, S.

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	--

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

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.