PDB-2gfn: Crystal structure of HTH-type transcriptional regulator pksA rela...

ID or keywords:

Entry

Database: PDB / ID: 2gfn

Title

Crystal structure of HTH-type transcriptional regulator pksA related protein from Rhodococcus sp. RHA1

Components

HTH-type transcriptional regulator pksA related protein

Keywords

TRANSCRIPTION / hth-type transcriptional regulator / transcriptional regulator tetr / PSI-2 / Regulatory protein / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

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

Biological species

Rhodococcus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Nocek, B. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of HTH-type transcriptional regulator pksA related protein from Rhodococcus sp. RHA1
Authors: Nocek, B. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Mar 22, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE There is currently no aminoacid sequence database reference available for this protein

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gfn.cif.gz	92.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2gfn.ent.gz	72.7 KB	Display	PDB format
PDBx/mmJSON format	2gfn.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/gf/2gfn ftp://data.pdbj.org/pub/pdb/validation_reports/gf/2gfn	HTTPS FTP

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Related structure data

Similar structure data	6srn-1 3vib-1 5f27-1 1jty-1 3bti-1 1qvt-1 3btl-1 1jus-1 4jnn-1 5niz-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC6003

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HTH-type transcriptional regulator pksA related protein

B: HTH-type transcriptional regulator pksA related protein

hetero molecules

45.2 kDa, 2 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)	56.475, 52.768, 59.818
Angle α, β, γ (deg.)	90.00, 91.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	VAL	VAL	A	A	5 - 198	5 - 198
2	HIS	HIS	B	B	7 - 198	7 - 198

Details

The asymmetric unit contains dimer, which is consistent with number of Tet-R like regulators determined to date.

#1: Protein	HTH-type transcriptional regulator pksA related protein Mass: 22600.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5YVI4, UniProt: Q0S7R9*PLUS
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / 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: 1.97 Å³/Da / Density % sol: 37.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG2K MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9795, 0.97934, 0.97948

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2006 / Details: mirrors

Radiation

Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9795	1
2	0.97934	1
3	0.97948	1

Reflection

Resolution: 1.9→30 Å / Num. all: 31193 / Num. obs: 30702 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / R_merge(I) obs: 0.097 / Net I/σ(I): 18.86

Reflection shell

Resolution: 1.9→1.95 Å / Redundancy: 3 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 99.12

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
Coot		model building
CCP4		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.9→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / SU B: 6.324 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21482	1416	5.1 %	RANDOM
R_work	0.17306	-	-	-
all	0.1752	27895	-	-
obs	0.1752	26479	99.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.838 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.24 Å²	0 Å²	1.23 Å²
2-	-	-1.49 Å²	0 Å²
3-	-	-	0.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2915	0	1	272	3188

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3001
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.402	1.96	4071
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.135	5	392
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.159	21.583	139
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.309	15	498
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.283	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	482
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2282
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1489
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	2149
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	190
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.18	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.17	0.2	17
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.921	1.5	2000
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.385	2	3068
X-RAY DIFFRACTION	r_scbond_it	2.181	3	1125
X-RAY DIFFRACTION	r_scangle_it	3.365	4.5	1003
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1362 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.59	0.5
medium thermal	1.18	2

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.244	109	-
R_work	0.196	1930	-
obs	-	-	99.12 %

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	85.2205	-46.7128	-3.7132	113.602	18.4709	3.2315	-1.0921	0.7517	-1.7499	2.624	1.5062	-1.7823	1.9654	-0.3378	-0.4141	0.1841	-0.0081	0.0441	-0.0321	0.0264	0.2393	15.0198	28.2216	59.7108
2	3.6204	-1.524	-0.8761	2.7451	0.0557	1.0975	-0.0506	-0.1124	-0.008	-0.0527	0.1213	0.273	0.0437	-0.0804	-0.0707	-0.02	0.0091	-0.0046	0.0621	-0.0296	0.1004	20.4348	39.3558	46.9715
3	7.4834	-1.4106	1.1301	1.8026	-1.0146	1.3475	-0.3442	-0.6508	0.339	-0.0467	0.232	-0.0598	0.0141	-0.2531	0.1122	-0.0026	0.0377	0.014	0.1048	-0.0802	0.0871	19.3488	44.5304	52.5258
4	1.3381	-0.5037	0.0511	11.9017	2.2794	0.4531	-0.1197	-0.1397	-0.4096	0.4612	0.1985	0.9201	-0.0323	-0.1491	-0.0788	-0.024	-0.0019	0.0508	0.108	0.0267	0.2439	21.8162	22.6379	50.1373
5	0.6822	-1.3661	0.4124	5.2692	-1.0104	0.2627	0.208	0.1229	-0.4323	-0.2071	-0.1691	0.7203	0.0076	-0.1588	-0.0389	0.0113	-0.0051	-0.0845	0.0793	-0.0716	0.2564	26.511	12.8786	42.0661
6	3.3743	-0.1964	0.9928	4.6783	2.5777	1.7805	0.1459	-0.0803	0.1017	-0.0247	-0.0418	-0.0425	0.1535	-0.0555	-0.1041	-0.0333	0.0101	0.0097	0.0568	-0.0169	0.0715	31.393	31.3682	46.7123
7	3.6618	0.4964	1.1042	10.536	4.5294	2.1653	0.1841	-0.2882	-0.1484	0.5525	-0.3523	0.1001	0.0821	-0.2313	0.1682	0.0619	-0.0636	0.0269	0.1156	0.0413	0.0115	32.0711	21.1797	55.2028
8	6.4207	2.918	1.4398	7.8356	1.6775	2.1515	0.4055	-0.226	-0.628	0.5531	-0.1854	0.1502	0.2473	-0.099	-0.22	0.0203	-0.0193	-0.0387	0.0524	0.0467	0.2384	34.7001	1.8405	50.9512
9	1.3663	0.0132	0.3698	2.9776	-1.2972	1.5398	0.127	0.0886	-0.2052	-0.2599	-0.1291	0.2243	0.0511	0.0004	0.0021	0.025	0.0584	-0.0379	0.0759	-0.0455	0.0376	36.8228	18.6916	38.6901
10	11.5148	-3.8014	-18.3896	2.0631	9.1279	40.9315	0.7566	0.9064	-2.1587	0.6179	0.2041	-2.1632	2.2221	-1.0773	-0.9606	0.1119	0.15	-0.0999	0.1403	-0.0752	0.4231	39.4001	4.5092	41.5748
11	3.4258	3.8444	-2.0643	5.4185	-2.9232	3.7315	0.0055	-0.0402	0.1393	0.1934	-0.1857	-0.1049	-0.0574	0.0185	0.1801	-0.0114	-0.0154	-0.0039	0.0919	-0.0511	0.0355	59.4662	41.8897	48.4129
12	4.4487	3.5516	-0.1146	4.8654	-0.5746	0.5005	0.2283	-0.3387	0.5338	0.485	-0.3552	0.283	-0.0987	-0.0551	0.1269	0.0584	-0.0056	0.0467	0.1123	-0.1199	0.064	56.2295	47.119	55.0399
13	1.3131	0.731	0.4003	4.6925	0.8492	1.4026	-0.0276	0.0092	0.2911	-0.2032	-0.1107	0.1898	-0.0606	-0.1632	0.1383	-0.0505	0.0123	-0.0034	0.0652	-0.0268	0.08	53.8308	44.389	44.3426
14	0.6548	0.3109	-0.1095	2.7025	0.8552	0.3788	0.094	-0.1603	-0.041	-0.0458	-0.0169	-0.2382	0.0271	0.0896	-0.0771	-0.0172	0.0165	0.0217	0.0763	0.0068	0.0169	56.9885	23.8852	43.4043
15	1.9082	-3.1902	-4.1517	16.1009	2.2972	11.036	0.7316	-0.3626	0.3951	-1.8454	-0.53	0.5546	-0.4882	-0.4329	-0.2016	0.0854	0.0797	-0.032	-0.0579	-0.0278	0.1731	40.4805	37.5523	38.7216
16	5.2021	-1.4884	-2.228	0.4306	0.5289	3.4427	0.3879	-0.0676	0.1413	-0.4276	-0.2622	-0.306	-0.4995	0.0626	-0.1257	0.1388	0.0347	0.0727	-0.0037	0.0137	-0.0014	49.0551	31.1916	35.6927
17	0.2441	-1.2821	-0.7666	6.7622	4.1958	3.4554	0.0342	-0.006	0.0071	-0.0531	0.0209	-0.2601	0.0587	0.0736	-0.055	0.0436	0.0144	0.0299	0.0527	-0.0073	0.012	53.875	14.2423	31.3823
18	0.5795	0.6692	-0.1104	1.1878	0.7598	2.1886	-0.0208	0.004	-0.0634	-0.0819	-0.0709	0.0467	0.1191	-0.097	0.0917	0.0235	0.0174	-0.006	0.0619	-0.0078	0.0162	45.3369	17.0847	39.0258
19	3.7172	-2.2358	-3.8311	7.617	3.4135	4.1446	-0.1594	-0.1619	-0.0896	0.9945	-0.0608	0.0288	0.619	0.1985	0.2201	0.1108	-0.0013	0.0004	0.098	0.0339	-0.0498	48.6565	16.786	55.3584
20	10.0765	-0.1519	5.2205	7.1121	3.7315	4.7466	0.2628	-0.0041	-0.585	0.2687	0.0286	0.1754	0.3146	-0.1951	-0.2914	0.0702	-0.0026	0.0078	0.0202	0.0189	0.0249	48.2783	8.4372	41.5535

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	4 - 7	4 - 7
2	X-RAY DIFFRACTION	2	A	A	8 - 35	8 - 35
3	X-RAY DIFFRACTION	3	A	A	36 - 56	36 - 56
4	X-RAY DIFFRACTION	4	A	A	57 - 78	57 - 78
5	X-RAY DIFFRACTION	5	A	A	79 - 98	79 - 98
6	X-RAY DIFFRACTION	6	A	A	99 - 115	99 - 115
7	X-RAY DIFFRACTION	7	A	A	120 - 137	120 - 137
8	X-RAY DIFFRACTION	8	A	A	138 - 156	138 - 156
9	X-RAY DIFFRACTION	9	A	A	157 - 195	157 - 195
10	X-RAY DIFFRACTION	10	A	A	196 - 199	196 - 199
11	X-RAY DIFFRACTION	11	B	B	7 - 24	7 - 24
12	X-RAY DIFFRACTION	12	B	B	25 - 45	25 - 45
13	X-RAY DIFFRACTION	13	B	B	46 - 67	46 - 67
14	X-RAY DIFFRACTION	14	B	B	68 - 111	68 - 111
15	X-RAY DIFFRACTION	15	B	B	112 - 122	112 - 122
16	X-RAY DIFFRACTION	16	B	B	123 - 131	123 - 131
17	X-RAY DIFFRACTION	17	B	B	132 - 149	132 - 149
18	X-RAY DIFFRACTION	18	B	B	150 - 174	150 - 174
19	X-RAY DIFFRACTION	19	B	B	175 - 189	175 - 189
20	X-RAY DIFFRACTION	20	B	B	190 - 199	190 - 199

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