PDB-7xxs: HapR mutant I141V

ID or keywords:

Entry

Database: PDB / ID: 7xxs

Title

HapR mutant I141V

Components

Hemagglutinin/protease regulatory protein

Keywords

TRANSCRIPTION / HapR Master Regulator

Function / homology

Function and homology information

peptidase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / proteolysis
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Basu Choudhury, G. / Chaudhari, V. / Ray Chaudhuri, S. / Datta, S.

Funding support

India, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2023
Title: Diversity in the ligand binding pocket of HapR attributes to its uniqueness towards several inhibitors with respect to other homologues - A structural and molecular perspective.
Authors: Sen, H. / Choudhury, G.B. / Pawar, G. / Sharma, Y. / Bhalerao, S.E. / Chaudhari, V.D. / Datta, S. / Raychaudhuri, S.

History

Deposition	May 30, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7xxs_validation.pdf.gz	438.8 KB	Display	wwPDB validaton report
Full document	7xxs_full_validation.pdf.gz	445.5 KB	Display
Data in XML	7xxs_validation.xml.gz	16.6 KB	Display
Data in CIF	7xxs_validation.cif.gz	22.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xx/7xxs ftp://data.pdbj.org/pub/pdb/validation_reports/xx/7xxs	HTTPS FTP

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Related structure data

Related structure data	7xxnC 7xxoSC 7xxtC 7xy0C 7xy5C 7xyiC 7y4jC S: Starting model for refinement C: citing same article (ref.)
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

A: Hemagglutinin/protease regulatory protein

B: Hemagglutinin/protease regulatory protein

47.4 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

Unit cell

Length a, b, c (Å)	44.718, 85.331, 110.622
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Hemagglutinin/protease regulatory protein / TetR/AcrR family transcriptional regulator Mass: 23708.365 Da / Num. of mol.: 2 / Mutation: I141V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: hapR, D6U24_16025, ERS013186_00946, ERS013198_01284, ERS013202_02486 Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2CKP3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 70 / 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: 46.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 7% PEG 8000, 100 mM CHES pH 9.5, 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: Apr 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.25→28.45 Å / Num. obs: 134666 / % possible obs: 99 % / Redundancy: 6.5 % / CC_1/2: 0.999 / Net I/σ(I): 18.4
Reflection shell	Resolution: 2.25→2.33 Å / Redundancy: 6.4 % / Num. unique obs: 2033 / CC_1/2: 0.92 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.27	data extraction
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XXO

7xxo

Resolution: 2.25→28.449 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2767	3768	9.73 %
R_work	0.2333	34971	-
obs	0.2375	38739	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 119.01 Å² / B_iso mean: 52.8792 Å² / B_iso min: 23.54 Å²

Refinement step

Cycle: final / Resolution: 2.25→28.449 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3237	0	0	70	3307
B_iso mean	-	-	-	46.85	-
Num. residues	-	-	-	-	395

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
2.2501-2.2786	0.3801	135	0.3242	1277
2.2786-2.3085	0.3024	138	0.3192	1297
2.3085-2.3401	0.2955	142	0.3067	1331
2.3401-2.3736	0.3279	137	0.3149	1264
2.3736-2.409	0.3357	136	0.2987	1304
2.409-2.4466	0.3079	142	0.3168	1309
2.4466-2.4867	0.2942	139	0.3044	1315
2.4867-2.5295	0.2802	138	0.2916	1271
2.5295-2.5755	0.3639	138	0.277	1295
2.5755-2.625	0.3594	137	0.286	1323
2.625-2.6785	0.3163	143	0.2814	1295
2.6785-2.7367	0.3092	131	0.2869	1275
2.7367-2.8003	0.3513	142	0.273	1332
2.8003-2.8703	0.302	134	0.2728	1239
2.8703-2.9478	0.3286	142	0.2973	1325
2.9478-3.0345	0.3094	140	0.289	1293
3.0345-3.1323	0.2955	143	0.2453	1297
3.1323-3.2441	0.2455	140	0.2491	1290
3.2441-3.3738	0.289	140	0.2413	1277
3.3738-3.5271	0.2796	143	0.2283	1301
3.5271-3.7127	0.2402	141	0.2104	1320
3.7127-3.9447	0.2407	139	0.2065	1258
3.9447-4.2484	0.233	144	0.1849	1306
4.2484-4.6742	0.2139	141	0.1797	1274
4.6742-5.3467	0.2626	146	0.1924	1311
5.3467-6.7216	0.2689	137	0.2316	1298
6.7216-28	0.2746	140	0.1674	1294

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	5.3307	-0.8274	1.844	5.5647	-1.7347	3.763	-0.5363	-1.2105	-1.1663	0.639	0.5114	0.8514	0.0599	-0.3368	-0.3911	0.443	-0.0321	0.1711	0.4532	0.1888	0.5003	-12.3309	-23.2111	37.4715
2	7.806	-2.4092	3.2517	7.0218	-2.8513	4.9576	-0.0568	0.1871	-0.2106	-0.236	0.0484	-0.0674	-0.4597	-0.1178	0.0946	0.4484	-0.0669	0.0566	0.4384	-0.0166	0.2055	-6.7308	-17.7641	30.9479
3	6.6398	-0.3881	3.8911	6.7592	-2.4273	4.8867	-0.5748	-1.4371	0.3729	1.2297	0.3302	-0.2437	-1.2804	-1.1021	0.301	0.7001	0.0833	-0.1146	0.3417	-0.0855	0.3872	-4.2925	-13.922	38.3768
4	2.6305	-1.077	-0.4061	2.2839	-1.9019	4.9558	-0.103	-0.1934	0.1841	0.3565	-0.3267	-0.7315	-0.2074	1.0382	-0.0246	0.3294	-0.0641	-0.1052	0.3369	0.0571	0.3541	-0.487	-13.1451	20.5709
5	4.0713	-0.1078	-1.5148	4.6983	-0.5064	7.8389	-0.055	0.1458	-0.1714	-0.0965	-0.0535	0.0578	0.0258	-0.3021	0.0345	0.2428	-0.0129	-0.0282	0.1688	-0.0185	0.2304	-9.5365	-12.686	9.6565
6	3.9135	-0.9797	0.2117	3.4398	-1.3672	2.4014	0.5339	-0.614	0.2328	0.3389	-0.1373	-1.1506	-0.7039	0.764	-0.2035	0.5233	-0.184	-0.1084	0.4674	0.0148	0.4432	1.6837	-3.5314	10.7058
7	3.5996	0.5903	-1.2598	5.0638	2.0001	5.5533	0.139	0.1814	0.2001	-0.2386	0.0315	-0.0563	-0.5662	-0.1549	-0.1837	0.4079	0.0021	-0.0512	0.2458	-0.0551	0.2971	-8.6467	-3.0377	4.0286
8	9.2356	-1.7559	-3.3389	5.8304	1.2182	6.3754	-0.1208	1.0177	-0.9345	-0.7416	-0.0058	0.4978	0.7051	-1.1215	-0.1376	0.5153	0.0283	-0.2119	0.4326	-0.0455	0.3781	-17.903	-7.0604	1.0518
9	8.0547	-2.2994	-0.6195	3.4704	0.007	5.0279	0.0171	0.6219	2.4043	0.0548	-0.0477	-1.8584	-0.9435	0.3373	-0.3459	0.4968	-0.1779	0.0949	0.4905	-0.0195	0.8738	-9.7445	25.8861	36.9417
10	8.5257	-1.5605	-1.5088	6.1013	2.3586	6.7634	-0.005	0.8844	-0.0066	0.0326	0.1471	-0.4198	0.3019	0.857	-0.1459	0.226	0.0334	0.0339	0.5913	0.0263	0.2212	-14.5698	16.5844	33.7302
11	1.6947	-1.0583	-2.2992	2.8052	2.0745	8.0022	0.0707	-0.078	-0.157	0.0183	-0.0626	0.1583	-0.0827	-0.5428	0.1951	0.244	0.0347	-0.0172	0.3192	-0.034	0.2595	-21.6684	16.2098	29.091
12	4.4448	-0.526	-0.1426	4.0741	0.7142	5.3595	0.1089	0.2173	0.6496	-1.3128	-0.2219	-0.3199	-0.3928	-0.1246	0.1123	0.4882	0.1331	0.1096	0.2467	0.1069	0.1833	-14.354	14.4674	11.1236
13	5.0626	3.0123	0.3	3.5191	-0.1819	7.3777	0.6743	-1.0449	-0.0921	1.6922	-0.6937	-0.1775	1.1912	-0.6729	-0.1978	1.1635	-0.3151	0.1299	0.8283	0.0034	0.6033	-23.4163	0.7348	22.3376
14	7.557	3.0822	-2.0493	7.6382	1.8285	4.2567	-0.0039	0.7207	0.7144	0.2509	0.0038	1.4421	-0.3387	-1.5522	-0.1286	0.7682	0.2998	0.0476	0.7158	0.102	0.5569	-27.6365	9.6624	4.2775
15	3.6237	0.9787	-1.1198	3.5723	1.1073	7.0926	-0.1922	1.3846	0.0154	-0.8873	0.1524	1.1765	-0.4547	-1.4503	0.2299	1.4351	-0.3109	-0.4603	1.2588	0.2161	0.5948	-24.3904	4.9088	-6.308
16	4.2003	3.4118	-0.0934	7.2474	1.2953	6.404	0.1673	0.1254	0.157	-0.6069	0.102	-0.1143	-1.0897	0.2983	-0.2247	0.4941	0.0499	0.1173	0.2372	0.0266	0.3263	-9.2865	8.0017	6.591

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 14 )	A	4 - 14
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 33 )	A	15 - 33
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 60 )	A	34 - 60
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 83 )	A	61 - 83
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 119 )	A	84 - 119
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 150 )	A	120 - 150
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 151 through 181 )	A	151 - 181
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 182 through 202 )	A	182 - 202
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 5 through 14 )	B	5 - 14
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 15 through 47 )	B	15 - 47
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 48 through 83 )	B	48 - 83
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 120 )	B	84 - 120
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 121 through 134 )	B	121 - 134
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 135 through 150 )	B	135 - 150
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 151 through 159 )	B	151 - 159
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 160 through 200 )	B	160 - 200

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