PDB-3k3c: The N-terminal PAS domain crystal structure of Rv1364c from Mycob...

ID or keywords:

Entry

Database: PDB / ID: 3k3c

Title

The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62

Components

Protein Rv1364c/MT1410

Keywords

SIGNALING PROTEIN / Sensor / PAS / signal transduction / fatty-acid binding / sigma factor regulator

Function / homology

Function and homology information

alkaline phosphatase activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / protein serine/threonine/tyrosine kinase activity / manganese ion binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.62 Å

Authors

King-Scott, J. / Tucker, P.A.

Citation

Journal: To be Published
Title: The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62
Authors: King-Scott, J. / Tucker, P.A.

History

Deposition	Oct 2, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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	3k3c.cif.gz	157.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3k3c.ent.gz	126.5 KB	Display	PDB format
PDBx/mmJSON format	3k3c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3k3c_validation.pdf.gz	941.6 KB	Display	wwPDB validaton report
Full document	3k3c_full_validation.pdf.gz	954.4 KB	Display
Data in XML	3k3c_validation.xml.gz	17.4 KB	Display
Data in CIF	3k3c_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/3k3c ftp://data.pdbj.org/pub/pdb/validation_reports/k3/3k3c	HTTPS FTP

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Related structure data

Related structure data	3k3d
Similar structure data	2vqr-d 6n6j-d 4hpp-d 5y5q-d 3fi1-d 2fxq-1 2ffk-d 1maa-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3k3d

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (6) #207 - Mar 2017 Photoactive Yellow Protein similarity (2) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Protein Rv1364c/MT1410

B: Protein Rv1364c/MT1410

C: Protein Rv1364c/MT1410

D: Protein Rv1364c/MT1410

hetero molecules

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

1

A: Protein Rv1364c/MT1410

B: Protein Rv1364c/MT1410

hetero molecules

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

2

C: Protein Rv1364c/MT1410

D: Protein Rv1364c/MT1410

hetero molecules

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

3

A: Protein Rv1364c/MT1410

D: Protein Rv1364c/MT1410

hetero molecules

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

4

B: Protein Rv1364c/MT1410

C: Protein Rv1364c/MT1410

hetero molecules

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

5

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	209.069, 63.823, 61.305
Angle α, β, γ (deg.)	90.00, 89.95, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-621- HOH
2	1	D-174- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D

NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	LEU	LEU	A	A	-1 - 52	1 - 54
2	1	1	GLY	GLY	LEU	LEU	B	B	-1 - 52	1 - 54
1	2	1	GLY	GLY	ARG	ARG	A	A	56 - 113	58 - 115
2	2	1	GLY	GLY	ARG	ARG	B	B	56 - 113	58 - 115
1	3	1	ARG	ARG	SER	SER	A	A	114 - 119	116 - 121
2	3	1	ARG	ARG	SER	SER	B	B	114 - 119	116 - 121
1	4	1	ILE	ILE	ALA	ALA	A	A	120 - 142	122 - 144
2	4	1	ILE	ILE	ALA	ALA	B	B	120 - 142	122 - 144
1	5	1	ARG	ARG	ARG	ARG	A	A	143 - 150	145 - 152
2	5	1	ARG	ARG	ARG	ARG	B	B	143 - 150	145 - 152
1	1	2	ASP	ASP	PRO	PRO	C	C	6 - 50	8 - 52
2	1	2	ASP	ASP	PRO	PRO	D	D	6 - 50	8 - 52
1	2	2	LEU	LEU	LEU	LEU	C	C	51 - 52	53 - 54
2	2	2	LEU	LEU	LEU	LEU	D	D	51 - 52	53 - 54
1	3	2	THR	THR	SER	SER	C	C	54 - 99	56 - 101
2	3	2	THR	THR	SER	SER	D	D	54 - 99	56 - 101
1	4	2	GLY	GLY	GLU	GLU	C	C	100 - 149	102 - 151
2	4	2	GLY	GLY	GLU	GLU	D	D	100 - 149	102 - 151
1	5	2	ARG	ARG	VAL	VAL	C	C	150 - 154	152 - 156
2	5	2	ARG	ARG	VAL	VAL	D	D	150 - 154	152 - 156

NCS ensembles :

ID
1
2

#1: Protein	Protein Rv1364c/MT1410 Mass: 17927.793 Da / Num. of mol.: 4 / Fragment: UNP residues 1-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1410, MTCY02B10.28c, Rv1364c / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRPpLysS / References: UniProt: Q11034, UniProt: P9WLZ7*PLUS
#2: Chemical	ChemComp-PLM / PALMITIC ACID Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.87 %
Crystal grow	Temperature: 292.16 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.4 M ammonium sulphate, 0.1 M Tris-HCl, 0.1 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.16K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2006
Radiation	Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.808 Å / Relative weight: 1
Reflection	Resolution: 1.62→20 Å / Num. all: 101268 / Num. obs: 101268 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / B_iso Wilson estimate: 25.2 Å² / R_merge(I) obs: 0.087 / Net I/σ(I): 9
Reflection shell	Resolution: 1.62→1.65 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.654 / Mean I/σ(I) obs: 2.77 / Num. unique all: 4886 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
DENZO		data reduction
Auto-Rickshaw		phasing
REFMAC	5.2.0019	refinement
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.62→20 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.943 / SU B: 3.404 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21233	4927	5 %	RANDOM
R_work	0.181	-	-	-
all	0.183	98602	-	-
obs	0.183	93675	96.11 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.173 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.34 Å²	0 Å²	0 Å²
2-	-	0.45 Å²	0 Å²
3-	-	-	-0.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4824	0	132	657	5613

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	5457
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3893
X-RAY DIFFRACTION	r_angle_refined_deg	1.437	1.968	7448
X-RAY DIFFRACTION	r_angle_other_deg	1.123	3.002	9278
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.415	5	702
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.965	22.785	316
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.764	15	903
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.686	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.165	0.2	770
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6260
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1238
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	1203
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	4590
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	2629
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	3139
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	582
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.16	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.26	0.2	103
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.181	0.2	41
X-RAY DIFFRACTION	r_mcbond_it	1.177	1.5	4181
X-RAY DIFFRACTION	r_mcbond_other	0.19	1.5	1288
X-RAY DIFFRACTION	r_mcangle_it	1.433	2.5	5186
X-RAY DIFFRACTION	r_scbond_it	3.206	5	2605
X-RAY DIFFRACTION	r_scangle_it	4.315	10	2214

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	889	tight positional	0.02	0.05
2	C	889	tight positional	0.01	0.05
1	A	1302	medium positional	0.59	0.5
2	C	1303	medium positional	0.37	0.5
1	A	889	tight thermal	0.22	1.5
2	C	889	tight thermal	0.17	1.5
1	A	1302	medium thermal	0.56	2.5
2	C	1303	medium thermal	0.41	2.5

LS refinement shell

Resolution: 1.62→1.662 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	311	-
R_work	0.224	6519	-
obs	-	6830	91.25 %

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	0.2843	-0.0407	-0.0326	0.8386	-0.6924	0.7416	0.0326	0.0103	0.0188	0.0685	0.0446	0.165	-0.0101	-0.0735	-0.0772	-0.0054	-0.005	0.0199	-0.0472	-0.0087	0.0189	39.581	5.344	21.003
2	0.1726	-0.1239	-0.0782	0.672	0.1677	0.9601	0.023	0.0062	-0.0052	-0.0767	-0.0386	-0.0043	0.0493	-0.0101	0.0155	0.0167	-0.0005	-0.0018	-0.0766	-0.0019	-0.0062	52.48	-0.738	4.33
3	19.0139	1.0772	0.2463	0.1948	-0.4365	1.5205	0.0779	0.3258	0.5806	0.0417	-0.106	0.0778	-0.049	0.3556	0.028	-0.0612	-0.0242	0.0147	0.0389	0.0064	0.0227	78.678	12.235	4.705
4	0.2465	-0.0213	0.0189	0.9755	-0.7943	0.7601	0.0216	0.0029	-0.0075	-0.0512	0.0507	0.1581	0.0275	-0.0816	-0.0723	-0.0023	0.0011	-0.019	-0.0414	-0.0075	0.0166	39.573	7.885	9.613
5	0.123	0.0533	0.0584	0.7426	0.1604	1.0568	0.0259	0.0031	0.0048	0.0841	-0.0372	-0.0001	-0.0526	-0.0056	0.0113	0.012	-0.0004	0.0031	-0.0753	-0.0005	-0.0064	52.501	13.926	26.311
6	22.6595	-1.8099	0.0274	0.4787	-0.6441	1.2331	0.0625	-0.3689	-0.6251	-0.0163	-0.0842	0.1079	0.0105	0.3937	0.0217	-0.0553	0.0248	-0.0129	0.0538	-0.0007	0.0174	78.634	0.995	26.047
7	3.8984	0.165	1.7481	2.2118	-1.1861	5.1489	0.0593	0.1327	-0.1512	-0.1065	0.0641	-0.223	0.2239	0.5853	-0.1234	-0.1775	0.0492	0.0078	0.1935	-0.041	-0.0395	102.684	2.712	13.956
8	3.0077	-0.2521	0.4911	0.7383	-0.0872	3.2193	-0.0108	-0.1897	0.5968	0.0669	0.0558	-0.1284	-0.73	0.0791	-0.045	0.0039	-0.0018	0.0024	0.0816	-0.067	0.0234	90.459	18.914	23.97
9	7.2372	-2.3816	4.5041	1.0873	-1.5388	2.8471	-0.1135	0.01	0.271	0.0952	0.0199	-0.0426	-0.2315	0.2222	0.0936	-0.1121	-0.0035	-0.0076	0.175	-0.0085	-0.0384	89.252	12.577	24.757
10	6.8257	0.3753	1.5815	0.7529	-0.2027	1.9345	0.0208	-0.1867	0.019	-0.0514	0.0051	0.0274	-0.1246	-0.0065	-0.0258	0.0101	0.0015	0.0063	-0.0745	-0.0072	-0.0155	58.048	18.803	9.884
11	4.4458	-0.347	-1.5651	2.4641	-1.4804	5.8165	0.1174	-0.2494	0.1811	0.1288	0.02	-0.246	-0.2422	0.6839	-0.1374	-0.1821	-0.0471	-0.0023	0.1961	-0.0555	-0.0463	102.675	10.518	16.67
12	3.0792	0.327	-0.9951	0.737	-0.1084	3.0302	-0.0711	0.1808	-0.612	-0.0911	0.0694	-0.1387	0.6891	0.0882	0.0017	-0.0101	0.0128	0.0013	0.069	-0.0576	0.0265	90.504	-5.748	6.732
13	8.0406	2.8196	-5.3187	1.1685	-1.9106	3.5298	-0.1637	0.0316	-0.2956	-0.1144	0.0384	-0.0687	0.2518	0.2263	0.1253	-0.1145	0.0033	0.0079	0.1658	-0.0123	-0.0366	89.228	0.609	5.877
14	6.101	-0.68	-1.734	0.789	-0.2024	2.0089	0.0393	0.2294	-0.0413	0.0285	0.0009	0.0344	0.1408	-0.026	-0.0403	0.0064	-0.0053	-0.0034	-0.076	-0.004	-0.0107	58.067	-5.615	20.762

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 25
2	X-RAY DIFFRACTION	2	A	26 - 129
3	X-RAY DIFFRACTION	3	A	130 - 150
4	X-RAY DIFFRACTION	4	B	-1 - 25
5	X-RAY DIFFRACTION	5	B	26 - 129
6	X-RAY DIFFRACTION	6	B	130 - 150
7	X-RAY DIFFRACTION	7	C	5 - 23
8	X-RAY DIFFRACTION	8	C	24 - 92
9	X-RAY DIFFRACTION	9	C	101 - 128
10	X-RAY DIFFRACTION	10	C	131 - 154
11	X-RAY DIFFRACTION	11	D	5 - 23
12	X-RAY DIFFRACTION	12	D	24 - 92
13	X-RAY DIFFRACTION	13	D	101 - 128
14	X-RAY DIFFRACTION	14	D	131 - 154

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