PDB-7xy0: HapR Double mutant Y76F, F171C

ID or keywords:

Entry

Database: PDB / ID: 7xy0

Title

HapR Double mutant Y76F, F171C

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 / Resolution: 2.43 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 31, 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 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7xy0.cif.gz	177.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7xy0.ent.gz	142.6 KB	Display	PDB format
PDBx/mmJSON format	7xy0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7xy0_validation.pdf.gz	436.3 KB	Display	wwPDB validaton report
Full document	7xy0_full_validation.pdf.gz	443.4 KB	Display
Data in XML	7xy0_validation.xml.gz	17.1 KB	Display
Data in CIF	7xy0_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xy/7xy0 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xy0	HTTPS FTP

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Related structure data

Related structure data	7xxnC 7xxoC 7xxsC 7xxtC 7xy5C 7xyiC 7y4jC 2pbxS 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

47.3 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

Unit cell

Length a, b, c (Å)	43.699, 85.677, 109.838
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: 23662.361 Da / Num. of mol.: 2 / Mutation: Y76F, F171C 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: 2.17 Å³/Da / Density % sol: 43.4 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 12% PEG 8000, 100 mM Tris pH 8.5, 200 mM MgCl2

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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: Mar 26, 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: 2.43→26.11 Å / Num. obs: 30704 / % possible obs: 98 % / Redundancy: 12.4 % / CC_1/2: 0.99 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.43→2.52 Å / R_merge(I) obs: 0.952 / Num. unique obs: 1584

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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: 2pbx

2pbx

Resolution: 2.43→25.338 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2806	3004	10.02 %
R_work	0.2273	26966	-
obs	0.2327	29970	99.96 %

Solvent computation

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

Displacement parameters

B_iso max: 180.86 Å² / B_iso mean: 53.9375 Å² / B_iso min: 15.55 Å²

Refinement step

Cycle: final / Resolution: 2.43→25.338 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3221	0	0	70	3291
B_iso mean	-	-	-	36.77	-
Num. residues	-	-	-	-	394

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
2.4301-2.4699	0.3895	144	0.3349	1266
2.4699-2.5125	0.3511	141	0.3238	1309
2.5125-2.5581	0.3811	145	0.3054	1277
2.5581-2.6073	0.4133	149	0.3047	1292
2.6073-2.6604	0.3379	143	0.3145	1280
2.6604-2.7182	0.3984	142	0.3081	1270
2.7182-2.7814	0.3553	141	0.2782	1278
2.7814-2.8509	0.2889	150	0.2595	1301
2.8509-2.9278	0.3605	146	0.2736	1278
2.9278-3.0138	0.3563	141	0.2731	1258
3.0138-3.111	0.3257	151	0.2488	1333
3.111-3.2219	0.309	135	0.2427	1262
3.2219-3.3507	0.2937	142	0.246	1290
3.3507-3.5028	0.2512	144	0.2213	1263
3.5028-3.6869	0.292	146	0.2196	1299
3.6869-3.9171	0.2326	142	0.211	1285
3.9171-4.2183	0.2239	143	0.1881	1280
4.2183-4.6405	0.2352	141	0.1676	1273
4.6405-5.3066	0.2451	139	0.1809	1297
5.3066-6.6656	0.2433	135	0.2133	1283
6.6656-25.33	0.2094	144	0.1678	1292

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	2.1092	2.301	-0.0821	4.8496	1.6662	3.3363	-0.6133	-0.9075	-0.0646	1.0087	0.9125	-1.1107	0.8648	1.4037	-0.2842	0.6856	0.1149	-0.1461	0.3673	0.0662	0.3395	-3.8353	-7.174	-1.2985
2	2.2149	-1.9227	3.7527	3.2199	-2.0427	7.2041	-0.7228	0.1287	1.4045	0.231	1.28	3.4473	-1.831	-1.0901	-1.2957	0.7959	0.1906	0.3989	0.7167	0.2098	1.3351	-13.5276	26.2598	-36.9841
3	5.6017	0.3039	-0.8741	8.6402	-4.2155	8.1493	0.1831	-0.4334	-0.0271	-0.4233	0.1786	0.2869	0.2002	-0.0858	-0.4289	0.234	-0.0457	0.0211	0.4545	-0.0147	0.1331	-8.1283	16.7822	-33.5414
4	1.8424	-0.2714	-2.1532	3.6414	-1.9173	3.7466	-0.0324	-0.0203	-0.0597	0.1346	-0.1806	-0.131	-0.1917	0.7372	0.1719	0.2811	-0.1112	-0.0353	0.2771	-0.049	0.1831	-0.9788	16.674	-28.9558
5	5.1967	0.4079	0.745	2.4667	-2.4772	5.6789	-0.045	0.2337	0.2666	0.4436	-0.1853	0.0646	0.1871	0.4051	0.1596	0.5316	-0.0257	0.0261	0.2586	-0.0555	0.22	-7.2293	12.1882	-12.8633
6	3.0053	1.5342	-2.078	4.6087	4.105	9.3062	0.5555	0.0102	-0.1563	0.1523	-0.5835	-1.1619	-0.1743	0.8851	0.2424	0.5784	-0.0233	-0.0108	0.4575	0.1902	0.549	4.5912	8.049	-9.5115
7	2.0096	3.8816	-0.5193	5.4837	0.8722	1.9574	0.0299	-2.3316	-0.5362	2.1576	-1.3286	-0.8046	-1.1741	0.342	-0.244	1.1812	0.2091	-0.3218	0.8613	-0.0235	0.4377	2.1122	4.9432	6.3092
8	2.5203	-1.7871	-0.6327	4.761	-2.9499	5.0443	0.0861	0.0335	-0.0098	0.2028	0.0238	0.243	-0.5973	-0.2427	-0.0512	0.5197	0.027	0.0528	0.2009	-0.054	0.2446	-13.1724	7.9055	-6.5491
9	2.4992	1.434	0.6929	5.6788	0.6497	3.2428	-0.6612	1.2577	-0.3903	-0.4855	0.9791	-0.6471	-0.599	0.8168	-0.6988	0.64	0.2237	-0.0853	0.6955	-0.2527	0.7161	-9.6677	-23.8907	-37.6256
10	4.554	1.431	2.2869	4.195	3.1453	5.8287	-1.1402	0.8012	0.0016	-1.487	1.0033	0.1866	-1.6145	1.1256	0.2693	0.8025	-0.1716	-0.153	0.5311	0.0157	0.1725	-16.1847	-15.8292	-34.8973
11	2.4513	0.936	0.6324	2.7547	1.6653	2.2693	0.1825	-0.1394	-0.1387	-1.049	0.0615	0.7108	1.328	-1.3948	0.2485	0.6849	-0.0292	-0.1326	0.2915	-0.0816	0.2611	-20.9775	-13.4317	-20.4672
12	5.9229	-0.1823	-3.8611	3.1831	-1.0851	9.8849	0.3068	-0.3651	-0.3494	0.198	-0.2034	-0.11	0.176	0.5845	0.1174	0.4846	0.0082	-0.0268	0.1902	0.0115	0.2359	-11.6531	-14.4572	-3.5304
13	2.8986	-0.619	-0.6478	9.2016	-3.0021	5.4874	-0.2222	0.1618	-0.124	-0.587	0.0781	0.1429	-0.4796	-0.1866	0.1387	0.5812	0.0602	-0.1275	0.3178	0.0239	0.1535	-12.7961	-9.3214	-19.7428
14	4.1781	0.242	0.5697	4.4065	1.5188	2.1554	-0.3775	0.7965	1.3457	-1.198	0.5101	1.808	-0.0888	-0.0574	-0.4102	0.9559	0.1425	-0.2861	0.6925	0.1115	0.5281	-22.3393	0.2187	-21.0884
15	5.4124	0.9053	1.3704	7.254	1.3747	5.2964	0.9694	0.192	-0.1267	0.2941	-0.3259	0.6413	-0.1438	-0.5286	-0.2707	0.3879	0.1007	0.0739	0.3685	0.0163	0.3712	-24.9432	-7.4201	-2.1165
16	3.5233	0.3931	-2.4455	5.096	-3.1178	8.1679	0.2502	-0.1916	0.2561	-0.0155	0.0197	0.044	-0.2807	0.301	-0.2705	0.4415	0.0708	-0.0264	0.1992	0.0272	0.2298	-13.256	-2.9449	-4.0717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 182 through 202 )	B	182 - 202
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 5 through 14 )	A	5 - 14
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 15 through 47 )	A	15 - 47
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 83 )	A	48 - 83
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 126 )	A	84 - 126
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 127 through 150 )	A	127 - 150
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 151 through 159 )	A	151 - 159
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 160 through 200 )	A	160 - 200
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 60 )	B	15 - 60
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 61 through 83 )	B	61 - 83
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 107 )	B	84 - 107
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 119 )	B	108 - 119
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 134 )	B	120 - 134
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 135 through 150 )	B	135 - 150
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 151 through 181 )	B	151 - 181

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