PDB-4cic: T. potens IscR

ID or keywords:

Entry

Database: PDB / ID: 4cic

Title

T. potens IscR

Components

HEXA-ALANINE PEPTIDE
TRANSCRIPTIONAL REGULATOR, BADM/RRF2 FAMILY

Keywords

TRANSCRIPTION / TRANSCRIPTION REGULATION / DNA RECOGNITION / HELIX-TURN-HELIX MOTIF / RRF2-LIKE REGULATOR

Function / homology

Function and homology information

DNA-binding transcription factor activity / cytosol
Similarity search - Function

Biological species

THERMINCOLA POTENS (bacteria)
SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Santos, J.A. / Macedo-Ribeiro, S. / Pereira, P.J.B.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The Unique Regulation of Iron-Sulfur Cluster Biogenesis in a Gram-Positive Bacterium.
Authors: Santos, J.A. / Alonso-Garcia, N. / Macedo-Ribeiro, S. / Pereira, P.J.B.

History

Deposition	Dec 6, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 28, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 4, 2014	Group: Database references
Revision 1.2	Jun 25, 2014	Group: Database references
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cic.cif.gz	127.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4cic.ent.gz	101.4 KB	Display	PDB format
PDBx/mmJSON format	4cic.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/4cic ftp://data.pdbj.org/pub/pdb/validation_reports/ci/4cic	HTTPS FTP

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Related structure data

Related structure data	4chuC C: citing same article (ref.)
Similar structure data	3mh5-d 3dw0-d 6shg-d 4gfa-1 1otk-d 4lkm-d 4w6f-d 5jx3-4 Search similar-shape structures by Omokage search (details) 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: TRANSCRIPTIONAL REGULATOR, BADM/RRF2 FAMILY

B: TRANSCRIPTIONAL REGULATOR, BADM/RRF2 FAMILY

Q: HEXA-ALANINE PEPTIDE

hetero molecules

34.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.585, 53.585, 118.382
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (0.000368, -1, -0.000149), (-1, -0.000368, -0.000304), (0.000304, 0.000149, -1)
Vector: 133.9465, 133.9926, 56.4415)

#1: Protein	TRANSCRIPTIONAL REGULATOR, BADM/RRF2 FAMILY / ISCR Mass: 16832.299 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMINCOLA POTENS (bacteria) / Strain: JR / Plasmid: PETZ2_1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5X843
#2: Protein/peptide	HEXA-ALANINE PEPTIDE Mass: 444.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	STARTING MET RESIDUE REPLACED BY GAMGL DURING CLONING PROCEDURE. MUTATIONS C92S C101S C107S.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.4 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 0.1M BIS-TRIS PH 6.5 3M NACL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.6→53.6 Å / Num. obs: 43750 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / B_iso Wilson estimate: 26.44 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.6→1.69 Å / Redundancy: 4.5 % / R_merge(I) obs: 1.3 / Mean I/σ(I) obs: 1.6 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.6→48.817 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 28.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2203	1973	4.5 %
R_work	0.2021	-	-
obs	0.2029	43615	99.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→48.817 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2158	0	2	156	2316

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2249
X-RAY DIFFRACTION	f_angle_d	1.092	3031
X-RAY DIFFRACTION	f_dihedral_angle_d	15.339	847
X-RAY DIFFRACTION	f_chiral_restr	0.076	346
X-RAY DIFFRACTION	f_plane_restr	0.005	382

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 (%)
1.6005-1.6405	0.3549	136	0.3464	2875	X-RAY DIFFRACTION	97
1.6405-1.6849	0.3719	146	0.312	2971	X-RAY DIFFRACTION	99
1.6849-1.7344	0.3776	138	0.2729	2991	X-RAY DIFFRACTION	100
1.7344-1.7904	0.2812	141	0.2702	2946	X-RAY DIFFRACTION	100
1.7904-1.8544	0.2881	142	0.241	2992	X-RAY DIFFRACTION	100
1.8544-1.9287	0.2783	141	0.225	2955	X-RAY DIFFRACTION	100
1.9287-2.0165	0.2473	139	0.2102	2944	X-RAY DIFFRACTION	100
2.0165-2.1228	0.2524	137	0.2003	3021	X-RAY DIFFRACTION	100
2.1228-2.2558	0.2107	139	0.1799	2970	X-RAY DIFFRACTION	100
2.2558-2.4299	0.2074	145	0.1956	3003	X-RAY DIFFRACTION	100
2.4299-2.6744	0.2389	142	0.21	2988	X-RAY DIFFRACTION	100
2.6744-3.0614	0.2162	143	0.2157	2975	X-RAY DIFFRACTION	100
3.0614-3.8568	0.2119	142	0.1807	3004	X-RAY DIFFRACTION	100
3.8568-48.8396	0.1807	142	0.1867	3007	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	0.8733	0.1202	-0.0741	1.7037	0.4371	0.8027	0.0127	0.0194	0.0107	0.1401	0.1743	-0.0033	0.183	-0.2348	-0.0001	0.1855	0.0273	-0.0034	0.2236	0.0181	0.1729	70.7565	59.6884	14.8134
2	0.473	0.1488	0.2475	0.6321	0.3854	0.3198	0.077	0.0155	-0.1006	-0.2536	-0.1665	0.1774	0.2203	-0.0756	-0.003	0.1778	0.0111	0.0147	0.2771	-0.0272	0.2569	68.781	61.4332	0.936
3	0.1466	-0.0462	-0.0935	0.0587	-0.1561	0.8372	0.0107	0.5295	-0.4018	-0.0966	0.0842	-0.1531	-0.4364	-0.3844	0.0116	0.2314	0.0039	0.0299	0.191	-0.0122	0.2738	71.4198	71.2443	7.9533
4	0.5678	-0.6372	-0.0736	1.0163	0.3976	0.249	0.13	0.344	0.1445	-0.4354	-0.075	-0.4644	-0.3389	0.3429	0.0315	0.2485	-0.0405	0.0837	0.2722	-0.0049	0.3034	80.1667	68.4825	2.3218
5	0.818	0.2045	-0.2803	2.3096	0.4027	1.2053	0.0394	-0.0705	0.159	-0.1556	0.1115	-0.4065	-0.2129	0.386	0.0479	0.1502	-0.0175	0.0644	0.2401	-0.021	0.2024	80.8619	63.4738	5.8808
6	1.1536	0.7555	0.3027	0.9419	0.149	0.9395	0.3031	-0.4219	0.0104	-0.1387	-0.1921	0.1409	-0.277	-0.9457	0.0671	0.3898	-0.0564	-0.0161	0.1877	-0.0613	0.2405	84.0469	72.5729	40.8803
7	-0.0059	0.3278	0.5126	0.2444	0.5314	2.5202	-0.0658	-0.1171	-0.0185	0.0514	0.1899	-0.0542	0.0465	1.8039	-0.0102	0.2222	0.036	-0.0058	0.2958	-0.0046	0.1898	82.2839	59.4917	31.8546
8	0.6059	-0.7795	-0.2922	0.4276	0.2424	0.2172	-0.1408	0.1162	-0.2037	0.3542	-0.0213	0.1707	0.8276	-0.0074	-0.014	0.3215	-0.0184	0.0484	0.2466	-0.0433	0.2095	78.9609	49.1995	9.8042
9	1.6677	0.583	0.5194	1.4465	0.2459	0.1676	1.0688	-0.1462	-1.1606	0.3637	0.692	0.3611	-0.7171	0.0453	0.0347	1.042	0.2022	-0.1459	0.8313	-0.1116	0.6663	70.2423	38.3407	4.8678
10	0.042	-0.0325	0.0526	0.0561	0.0013	0.0464	-1.6081	-0.2752	-1.6776	-0.7407	-1.0445	-0.5706	0.4069	-1.4886	0.0035	0.6421	0.021	0.0716	0.8525	0.0602	1.2364	70.8081	28.6124	7.1152
11	1.104	-0.5354	-0.2875	1.305	-0.1421	0.635	0.149	0.0411	0.0052	0.0501	-0.0048	-0.0347	-0.3958	0.0096	-0.0004	0.2225	0.0016	0.0015	0.186	0.0066	0.1733	74.5119	63.0519	41.7615
12	0.3109	0.0412	0.5357	0.3817	0.4975	0.6408	-0.1533	-0.2984	0.1317	0.0225	0.045	0.0388	-0.1091	0.2261	-0.0179	0.2821	-0.0044	-0.0222	0.2057	-0.0001	0.2457	72.508	65.1642	55.5454
13	-0.0321	0.0171	-0.1067	0.3506	-0.2931	0.8704	0.0349	-0.1975	-0.2274	0.7976	0.0445	-0.3802	-0.4439	-0.4325	0.0063	0.2045	0.0092	-0.0112	0.215	0.0376	0.2987	62.6695	62.5135	48.5001
14	2.9036	0.0522	1.1223	1.223	-0.3058	1.1864	0.0431	-0.2016	-0.375	0.0863	-0.0026	0.1923	0.3884	-0.2527	0	0.2523	-0.0229	-0.0256	0.1552	0.0589	0.23	69.433	53.311	51.3718
15	0.5119	0.6687	-0.2016	0.5865	-0.1948	0.0302	-0.558	-0.3009	-0.4688	-0.257	0.4862	-0.037	-0.6994	-0.3029	-0.0334	0.3073	0.0229	-0.0812	0.3763	0.0294	0.2329	61.1262	49.791	15.358
16	0.5582	0.3024	0.7242	-0.0743	0.3139	4.7885	0.1223	0.1281	-0.0892	-0.0501	-0.0308	0.0066	1.8157	0.4013	-0.011	0.2561	0.038	0.0091	0.2017	-0.0187	0.1995	74.4268	51.6868	24.5295
17	0.4757	-0.8062	0.1805	0.5677	-0.0841	0.2895	0.0041	0.3706	0.1289	0.0543	0.0402	-0.1927	0.1541	0.9797	-0.0013	0.2233	-0.0037	-0.0304	0.335	0.0148	0.2098	84.7698	54.9953	46.7009
18	3.1538	3.2126	0.5509	4.151	-0.3528	0.4404	0.5261	-0.7109	-0.0404	0.3692	-1.1437	-2.789	-0.098	-0.4158	-0.2301	0.5911	-0.0061	-0.089	0.7242	0.1615	1.0074	100.9882	63.6615	50.9184
19	0.8823	-0.7361	0.9999	0.9387	-1.4165	2.1276	0.7525	-0.8808	1.3432	-0.0482	0.2153	1.2492	-0.0159	-0.4256	0.2225	0.4002	-0.02	-0.0081	0.3612	-0.0572	0.2717	71.159	63.5416	28.0427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -3 THROUGH 20 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 21 THROUGH 38 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 39 THROUGH 51 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 52 THROUGH 58 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 59 THROUGH 83 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 84 THROUGH 107 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 108 THROUGH 125 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 126 THROUGH 139 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 140 THROUGH 144 )
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 145 THROUGH 149 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID -3 THROUGH 20 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 21 THROUGH 38 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 39 THROUGH 51 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 52 THROUGH 83 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 84 THROUGH 107 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 108 THROUGH 125 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 126 THROUGH 139 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 140 THROUGH 148 )
19	X-RAY DIFFRACTION	19	CHAIN Q AND (RESID 10 THROUGH 15 )

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