PDB-9jrw: Quroum Sensing Master Regulator, HapR in Vibrio mimicus

ID or keywords:

Entry

Database: PDB / ID: 9jrw

Title

Quroum Sensing Master Regulator, HapR in Vibrio mimicus

Components

LuxR

Keywords

TRANSCRIPTION / Quroum Sensing Master regulator / HapR / Vibrio mimicus

Function / homology

: / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / transcription cis-regulatory region binding / DNA-binding transcription factor activity / LuxR

Function and homology information

Biological species

Vibrio mimicus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Choudhury, G.B. / Saha, A. / Datta, S. / Chauduri, S.R.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: HapR Homologues
Authors: Choudhury, G.B. / Dutta, S.

History

Deposition	Sep 29, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jrw.cif.gz	178.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9jrw.ent.gz	141.5 KB	Display	PDB format
PDBx/mmJSON format	9jrw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jrw_validation.pdf.gz	437.6 KB	Display	wwPDB validaton report
Full document	9jrw_full_validation.pdf.gz	444.8 KB	Display
Data in XML	9jrw_validation.xml.gz	20 KB	Display
Data in CIF	9jrw_validation.cif.gz	26.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jr/9jrw ftp://data.pdbj.org/pub/pdb/validation_reports/jr/9jrw	HTTPS FTP

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Related structure data

Related structure data	7xxoS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: LuxR

A: LuxR

47.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Homodimer

Unit cell

Length a, b, c (Å)	44.572, 85.282, 114.012
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	LuxR / HapR Mass: 23648.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio mimicus (bacteria) / Gene: luxRvm / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D2KZ16
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.31 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / Details: 20% PEG 8000, HEPES pH 7.5, 200 mM NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: Feb 4, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.15→27.39 Å / Num. obs: 55173 / % possible obs: 99 % / Redundancy: 5.1 % / B_iso Wilson estimate: 35.11 Å² / CC_1/2: 0.999 / Net I/σ(I): 13.1
Reflection shell	Resolution: 2.15→2.22 Å / Num. unique obs: 3821 / CC_1/2: 0.79

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XXO

7xxo

Resolution: 2.15→25.44 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2601	3749	8.22 %
R_work	0.2326	-	-
obs	0.2349	45582	99.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→25.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3246	0	0	131	3377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.583
X-RAY DIFFRACTION	f_dihedral_angle_d	3.903	430
X-RAY DIFFRACTION	f_chiral_restr	0.036	502
X-RAY DIFFRACTION	f_plane_restr	0.004	566

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.15-2.17	0.3738	126	0.3453	1409	X-RAY DIFFRACTION	93
2.17-2.2	0.3564	142	0.3328	1571	X-RAY DIFFRACTION	99
2.2-2.23	0.3629	144	0.3314	1603	X-RAY DIFFRACTION	100
2.23-2.27	0.3291	133	0.3153	1501	X-RAY DIFFRACTION	100
2.27-2.3	0.3771	146	0.3053	1579	X-RAY DIFFRACTION	100
2.3-2.34	0.2875	137	0.2972	1568	X-RAY DIFFRACTION	100
2.34-2.37	0.3137	136	0.2886	1543	X-RAY DIFFRACTION	100
2.37-2.41	0.3456	139	0.2789	1529	X-RAY DIFFRACTION	100
2.41-2.46	0.2869	142	0.2872	1569	X-RAY DIFFRACTION	100
2.46-2.51	0.2838	143	0.2763	1555	X-RAY DIFFRACTION	100
2.51-2.56	0.3359	134	0.2689	1547	X-RAY DIFFRACTION	100
2.56-2.61	0.3186	138	0.2831	1571	X-RAY DIFFRACTION	100
2.61-2.67	0.3718	138	0.2787	1572	X-RAY DIFFRACTION	100
2.67-2.74	0.3436	142	0.2736	1519	X-RAY DIFFRACTION	100
2.74-2.81	0.268	143	0.2626	1551	X-RAY DIFFRACTION	100
2.81-2.9	0.2552	137	0.2686	1545	X-RAY DIFFRACTION	100
2.9-2.99	0.3029	141	0.2629	1590	X-RAY DIFFRACTION	100
2.99-3.1	0.2712	142	0.2539	1534	X-RAY DIFFRACTION	100
3.1-3.22	0.2772	135	0.2454	1565	X-RAY DIFFRACTION	100
3.22-3.37	0.2621	138	0.2464	1547	X-RAY DIFFRACTION	100
3.37-3.54	0.2281	135	0.2173	1554	X-RAY DIFFRACTION	100
3.54-3.76	0.2388	143	0.2114	1544	X-RAY DIFFRACTION	100
3.77-4.05	0.2047	139	0.1907	1577	X-RAY DIFFRACTION	100
4.05-4.46	0.227	143	0.1852	1538	X-RAY DIFFRACTION	100
4.46-5.1	0.2126	138	0.1836	1561	X-RAY DIFFRACTION	100
5.1-6.41	0.2747	136	0.2159	1565	X-RAY DIFFRACTION	100
6.41-25.44	0.1782	139	0.1701	1526	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.4777	0.0019	-0.981	1.0672	-0.1862	1.0719	-0.1668	0.2458	0.2526	-0.2743	0.3846	0.1019	0.2859	-0.3175	0.0097	0.2875	-0.096	0.0084	0.3693	0.0448	0.2619	-7.1867	18.9933	-36.8031
2	0.2811	0.0021	-0.8797	0.7048	0.0053	2.5316	-0.0811	-0.3041	-0.3076	0.0421	-0.5563	-0.3255	-0.6325	1.1131	-0.3293	0.3407	-0.0896	-0.042	0.4036	0.1316	0.3878	-0.0148	15.419	-22.6916
3	1.4578	0.7539	-0.6236	1.1876	-1.3244	1.6439	0.028	0.0263	0.2987	0.4079	-0.0853	-0.2018	-0.5709	0.1056	-0.0064	0.2717	-0.0576	-0.0149	0.177	-0.0166	0.2304	-7.836	13.5235	-12.4314
4	1.5009	-0.9251	-0.0945	0.9407	-0.4403	0.5542	0.053	-0.2144	0.249	0.0954	-0.0554	-1.0173	-0.0523	0.9339	0.1398	0.4651	-0.1195	-0.1584	0.586	0.0149	0.6445	3.414	7.0238	-7.0351
5	0.3167	-0.0152	-0.2487	1.2326	-0.1285	0.771	-0.093	-0.137	0.2387	0.546	0.2812	0.0196	-0.3472	-0.2342	0.0519	0.323	0.0277	0.0008	0.2646	-0.0717	0.2708	-12.6745	7.9375	-6.0016
6	0.8999	0.5192	1.1009	1.7474	1.0977	1.4581	0.0462	0.1669	-0.0301	-0.1446	-0.0761	0.292	-0.341	0.1946	0.007	0.283	0.0006	-0.0176	0.2881	-0.0366	0.2582	-17.6053	-15.9852	-31.2591
7	0.8856	0.1588	0.3025	2.2131	0.7089	2.2179	-0.2484	-0.0593	-0.1372	0.2196	0.0702	0.279	0.0277	-0.3103	-0.0039	0.1818	0.0262	0.0159	0.2032	0.0095	0.2479	-18.0647	-7.8824	-8.092
8	0.6333	0.8197	0.3444	1.478	0.3158	0.4112	-0.0764	-0.1339	-0.0048	0.4424	0.3318	-0.281	0.1473	0.312	0.0174	0.3053	0.0876	-0.0487	0.2864	-0.0195	0.2725	-7.4859	-4.8837	-5.6877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 5 through 60 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 61 through 83 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 84 through 123 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 124 through 159 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 160 through 202 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 5 through 83 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 84 through 159 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 202 )

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