PDB-5whm: Crystal Structure of IclR Family Transcriptional Regulator from B...

ID or keywords:

Entry

Database: PDB / ID: 5whm

Title

Crystal Structure of IclR Family Transcriptional Regulator from Brucella abortus

Components

IclR family transcriptional regulator

Keywords

TRANSCRIPTION / helix-turn-helix / transcription factor / Chicago Center for Functional Annotation / Midwest Center for Structural Genomics / MCSG / PSI-Biology

Function / homology

ACETIC ACID / :

Function and homology information

Biological species

Brucella abortus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.95 Å

Authors

Kim, Y. / Wu, R. / Tesar, C. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI107792	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI107159	United States

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Molecular control of gene expression byBrucellaBaaR, an IclR-type transcriptional repressor.
Authors: Herrou, J. / Czyz, D.M. / Fiebig, A. / Willett, J.W. / Kim, Y. / Wu, R. / Babnigg, G. / Crosson, S.

History

Deposition	Jul 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0	Oct 25, 2017	Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 2.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5whm.cif.gz	437.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5whm.ent.gz	363.9 KB	Display	PDB format
PDBx/mmJSON format	5whm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5whm_validation.pdf.gz	474.2 KB	Display	wwPDB validaton report
Full document	5whm_full_validation.pdf.gz	483.1 KB	Display
Data in XML	5whm_validation.xml.gz	46.9 KB	Display
Data in CIF	5whm_validation.cif.gz	61.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wh/5whm ftp://data.pdbj.org/pub/pdb/validation_reports/wh/5whm	HTTPS FTP

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Related structure data

Similar structure data	3lzk-1 5wu7-1 2x2l-1 5xfm-1 4wiu-d 3lzk-2 4wpu-d 3bpw-d 4qyr-d 1xo2-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: IclR family transcriptional regulator

B: IclR family transcriptional regulator

C: IclR family transcriptional regulator

D: IclR family transcriptional regulator

hetero molecules

121 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: IclR family transcriptional regulator

C: IclR family transcriptional regulator

hetero molecules

defined by author&software
60.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: IclR family transcriptional regulator

D: IclR family transcriptional regulator

hetero molecules

defined by author&software
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.152, 112.462, 83.649
Angle α, β, γ (deg.)	90.00, 115.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	IclR family transcriptional regulator / IclR Mass: 30164.125 Da / Num. of mol.: 4 / Fragment: N-terminal deletion (UNP residues 21-284) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (bacteria) / Gene: BFJ58_02720 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) gold / References: UniProt: A0A1S1ZDZ5
#2: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₄O₂
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.64 Å³/Da / Density % sol: 53.45 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M calcium acetate, 0.1 M HEPES:NaOH, pH 7.5, 10% w/v PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97927 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 89094 / % possible obs: 99.4 % / Redundancy: 4.1 % / R_pim(I) all: 0.055 / R_sym value: 0.097 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 4102 / CC_1/2: 0.534 / R_pim(I) all: 0.517 / R_sym value: 0.742 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.95→33.556 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2123	4432	4.98 %	random
R_work	0.1772	-	-	-
obs	0.1789	88974	99.14 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→33.556 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8168	0	33	315	8516

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8551
X-RAY DIFFRACTION	f_angle_d	1.042	11586
X-RAY DIFFRACTION	f_dihedral_angle_d	18.194	5226
X-RAY DIFFRACTION	f_chiral_restr	0.061	1317
X-RAY DIFFRACTION	f_plane_restr	0.007	1517

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 (%)
1.95-1.9722	0.3894	145	0.3068	2394	X-RAY DIFFRACTION	87
1.9722-1.9954	0.2966	130	0.2857	2699	X-RAY DIFFRACTION	95
1.9954-2.0197	0.2897	129	0.2714	2812	X-RAY DIFFRACTION	99
2.0197-2.0453	0.2951	115	0.2545	2881	X-RAY DIFFRACTION	100
2.0453-2.0722	0.2879	152	0.2318	2814	X-RAY DIFFRACTION	100
2.0722-2.1006	0.2763	165	0.2173	2824	X-RAY DIFFRACTION	100
2.1006-2.1306	0.248	164	0.1972	2816	X-RAY DIFFRACTION	100
2.1306-2.1624	0.2231	149	0.1882	2850	X-RAY DIFFRACTION	100
2.1624-2.1962	0.2085	165	0.1946	2801	X-RAY DIFFRACTION	100
2.1962-2.2322	0.2355	136	0.1841	2832	X-RAY DIFFRACTION	100
2.2322-2.2706	0.2217	139	0.1849	2871	X-RAY DIFFRACTION	100
2.2706-2.3119	0.242	150	0.1804	2824	X-RAY DIFFRACTION	100
2.3119-2.3564	0.2264	152	0.1793	2821	X-RAY DIFFRACTION	100
2.3564-2.4045	0.2423	178	0.1869	2835	X-RAY DIFFRACTION	100
2.4045-2.4567	0.2521	154	0.189	2823	X-RAY DIFFRACTION	100
2.4567-2.5139	0.2302	144	0.178	2815	X-RAY DIFFRACTION	100
2.5139-2.5767	0.2424	168	0.1888	2830	X-RAY DIFFRACTION	100
2.5767-2.6463	0.2137	142	0.1763	2870	X-RAY DIFFRACTION	100
2.6463-2.7242	0.2261	135	0.1845	2839	X-RAY DIFFRACTION	100
2.7242-2.8121	0.2231	158	0.1867	2847	X-RAY DIFFRACTION	100
2.8121-2.9125	0.2371	145	0.1799	2826	X-RAY DIFFRACTION	100
2.9125-3.0291	0.2177	143	0.1921	2843	X-RAY DIFFRACTION	100
3.0291-3.1668	0.2439	156	0.1964	2821	X-RAY DIFFRACTION	100
3.1668-3.3336	0.2165	170	0.1889	2859	X-RAY DIFFRACTION	100
3.3336-3.5423	0.1965	152	0.1749	2848	X-RAY DIFFRACTION	100
3.5423-3.8154	0.2244	120	0.1718	2888	X-RAY DIFFRACTION	100
3.8154-4.1988	0.1994	131	0.1477	2861	X-RAY DIFFRACTION	100
4.1988-4.8048	0.146	136	0.1315	2873	X-RAY DIFFRACTION	100
4.8048-6.0478	0.1754	121	0.1673	2915	X-RAY DIFFRACTION	100
6.0478-33.5613	0.1788	188	0.1624	2710	X-RAY DIFFRACTION	94

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	3.3018	-1.1667	0.7109	3.5458	-1.4766	1.56	-0.013	0.0664	0.1064	0.1139	-0.0285	0.0758	-0.0383	0.0456	0.0612	0.1601	0.0074	0.0172	0.1251	-0.0214	0.1337	41.254	40.1943	43.7074
2	5.4359	-1.6402	0.5151	2.5494	-1.1143	3.3836	-0.1992	-0.2851	0.3819	0.5895	0.1529	-0.0146	-0.3897	-0.1123	0.1026	0.3104	0.0524	0.0158	0.3695	0.0398	0.4507	26.791	49.0612	42.6577
3	3.3375	-0.0003	-1.6776	8.4231	-2.8848	4.5769	0.0579	-0.7229	-1.4084	0.0641	-0.1316	0.3634	0.7175	-0.0361	0.0446	0.3429	-0.0466	0.0154	0.4853	0.2546	0.9496	16.6838	32.0901	43.6054
4	2.0641	-0.6801	0.1086	3.7766	-1.8159	8.8461	-0.1927	-0.4568	-0.8352	0.3918	-0.3975	0.6599	0.6348	-0.0959	0.5954	0.343	-0.0381	0.1287	0.6103	0.1179	0.884	7.738	39.1107	42.7827
5	4.6026	-0.228	0.3786	3.8594	1.0309	4.3407	0.0135	-0.207	0.3096	0.1283	0.0289	0.2977	0.0075	-0.2621	-0.066	0.1806	0.0379	0.0161	0.3542	0.0658	0.5201	16.5526	49.7969	40.5343
6	3.9868	-0.0557	-3.7607	4.088	1.2099	3.893	0.2378	0.929	-0.0962	-0.7936	-0.193	0.4939	-0.5237	-0.4449	0.1306	0.2882	0.0606	-0.0902	0.6222	0.0885	0.5726	18.467	51.4789	27.2232
7	2.3376	-0.6465	-1.1165	0.6919	0.7332	1.5376	0.0301	-0.0132	-0.0044	-0.165	-0.0785	0.0739	-0.2824	0.1824	0.1169	0.2818	-0.0677	-0.0253	0.2622	0.0186	0.188	16.6537	59.2304	81.6681
8	4.5437	0.2072	-0.5814	5.6662	1.2687	4.0252	-0.0211	-0.9016	0.035	0.7279	-0.0956	-0.6785	-0.1633	0.3598	0.0791	0.3245	-0.0256	-0.0972	0.4969	-0.0109	0.2755	36.9959	51.8501	76.4289
9	1.3889	-0.4767	1.4206	7.4645	-2.1535	1.8331	0.0484	0.0839	-0.1566	-0.3433	-0.3164	-1.6422	0.171	0.9841	0.1625	0.3643	0.0677	0.0664	0.5619	0.0785	0.6522	58.2315	25.5374	45.8368
10	1.499	0.1398	0.023	4.4598	0.5901	0.2712	0.078	0.1247	0.05	-0.459	-0.1051	0.1444	-0.0675	-0.0047	0.054	0.2891	0.049	-0.0023	0.2356	0.0286	0.1722	44.1869	39.7604	38.0229
11	1.1697	1.774	0.39	2.7752	0.0778	3.5762	-0.2985	0.5263	0.963	-0.133	0.277	0.316	-0.3002	-0.501	0.0248	0.2763	0.0395	-0.0168	0.2916	0.0877	0.3819	46.7911	54.4599	36.5079
12	5.8374	-0.522	-3.3016	6.0812	0.3014	4.1207	-0.4606	0.0533	-0.964	0.4981	0.326	-0.8314	0.796	0.1504	0.1119	0.2887	0.0513	-0.091	0.3116	-0.0544	0.4881	66.5254	43.0646	40.8543
13	1.8679	-1.9469	-2.3147	6.4158	5.0671	6.0417	-0.1223	-0.1256	-0.1218	0.0215	0.0666	-0.8407	-0.0941	0.4881	-0.084	0.1867	0.0089	-0.0658	0.4098	-0.0683	0.5209	71.1419	53.4671	40.7581
14	4.2183	0.5567	-0.1036	5.5402	0.3513	4.8185	0.1672	-0.1859	0.2777	0.3632	-0.0828	0.0615	-0.2304	0.0049	-0.0863	0.1526	-0.0071	0.0022	0.154	-0.0154	0.2287	57.2715	59.7912	45.2396
15	4.7885	0.6363	0.4093	4.4246	-0.2388	5.7296	-0.064	0.1917	0.264	-0.5176	0.1808	0.4491	-0.4992	-0.2756	-0.0581	0.4128	0.0006	-0.1039	0.2033	0.0157	0.2711	7.5455	69.2692	74.5416
16	2.2415	2.5421	-0.1108	5.4663	-0.3126	0.696	0.0384	0.1331	-0.2694	-0.2752	-0.005	-0.3216	0.1812	0.1742	-0.0675	0.4188	0.0122	-0.0195	0.3601	-0.0623	0.2796	9.4521	44.667	76.2306
17	6.1784	-2.2365	1.9063	6.4826	-0.7344	4.3579	-0.2062	0.1785	0.2606	-0.0954	0.0349	1.1326	-0.0742	-0.7165	0.056	0.3288	0.003	-0.0179	0.4678	-0.0104	0.7449	-13.3121	47.961	75.8616
18	5.769	-1.265	0.252	6.0629	-0.2147	4.6389	0.2393	0.4521	-0.4984	-0.4031	-0.0101	0.7451	0.5609	-0.2825	-0.0786	0.4279	-0.0539	-0.1018	0.2645	-0.0752	0.3946	-1.7376	35.0023	75.5777
19	4.6736	-1.5473	-0.9822	3.5286	2.4699	5.505	0.1418	-0.1231	-1.5685	0.1543	0.0282	1.5857	0.905	-0.8971	-0.1839	0.4789	-0.092	-0.1177	0.5064	0.0119	1.0234	32.2985	19.211	39.7464
20	2.4572	-0.778	0.4028	4.4742	-0.7434	1.4188	-0.0212	-0.3061	-0.1231	0.7447	-0.0112	0.815	0.0799	-0.349	-0.1191	0.3194	-0.0027	0.0898	0.2822	0.0683	0.2895	38.1097	29.7758	53.2756

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 50 through 109 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 110 through 150 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 151 through 179 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 180 through 197 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 198 through 244 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 245 through 261 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid -1 through 119 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 120 through 261 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid -2 through 17 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 18 through 129 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 130 through 150 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 151 through 179 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 180 through 197 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 198 through 261 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid -2 through 74 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 75 through 150 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 151 through 197 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 198 through 260 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid -2 through 17 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 18 through 49 )

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