PDB-3ke6: The crystal structure of the RsbU and RsbW domains of Rv1364c fro...

ID or keywords:

Entry

Database: PDB / ID: 3ke6

Title

The crystal structure of the RsbU and RsbW domains of Rv1364c from Mycobacterium tuberculosis

Components

Protein Rv1364c/MT1410

Keywords

UNKNOWN FUNCTION /

anti-sigma factor / anti-sigma factor antagonist /

phosphatase / pp2c /

serine kinase /

ATPase

Function / homology

Function and homology information

alkaline phosphatase activity / myosin phosphatase activity /

protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase /

phosphatase activity / protein serine/threonine/tyrosine kinase activity / manganese ion binding /

non-specific serine/threonine protein kinase /

phosphorylation / protein serine kinase activity ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

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

Citation

Journal: To be Published
Title: The crystal structure of the RsbU and RsbW domains of Rv1364c from Mycobacterium tuberculosis
Authors: King-Scott, J. / Panjikar, S. / Tucker, P.A.

History

Deposition	Oct 24, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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.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_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

-
Download

PDBx/mmCIF format	3ke6.cif.gz	144.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3ke6.ent.gz	112.8 KB	Display	PDB format
PDBx/mmJSON format	3ke6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ke/3ke6 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3ke6	HTTPS FTP

-
Related structure data

Related structure data	3k3c 3k3d
Similar structure data	5tkg-d 5x1h-6 5tkf-5 3qc3-d 1eqn-1 5tt8-2 6tu1-d 1a5w-1 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

3k3c

3k3d

Similar structure data

-
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)

Deposited unit

A: Protein Rv1364c/MT1410

B: Protein Rv1364c/MT1410

hetero molecules

85.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein Rv1364c/MT1410

hetero molecules

defined by author
42.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein Rv1364c/MT1410

hetero molecules

defined by author
42.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: Protein Rv1364c/MT1410

hetero molecules

B: Protein Rv1364c/MT1410

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.118, 100.118, 169.653
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-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	GLY	GLY	ALA	ALA	A	A	175 - 185	35 - 45
2	1	GLY	GLY	ALA	ALA	B	B	175 - 185	35 - 45
1	2	GLY	GLY	GLY	GLY	A	A	193 - 202	53 - 62
2	2	GLY	GLY	GLY	GLY	B	B	193 - 202	53 - 62
1	3	ARG	ARG	VAL	VAL	A	A	204 - 212	64 - 72
2	3	ARG	ARG	VAL	VAL	B	B	204 - 212	64 - 72
1	4	GLU	GLU	ALA	ALA	A	A	218 - 236	78 - 96
2	4	GLU	GLU	ALA	ALA	B	B	218 - 236	78 - 96
1	5	VAL	VAL	LYS	LYS	A	A	240 - 252	100 - 112
2	5	VAL	VAL	LYS	LYS	B	B	240 - 252	100 - 112
1	6	SER	SER	PHE	PHE	A	A	259 - 269	119 - 129
2	6	SER	SER	PHE	PHE	B	B	259 - 269	119 - 129
1	7	SER	SER	ALA	ALA	A	A	271 - 279	131 - 139
2	7	SER	SER	ALA	ALA	B	B	271 - 279	131 - 139
1	8	PRO	PRO	ALA	ALA	A	A	282 - 289	142 - 149
2	8	PRO	PRO	ALA	ALA	B	B	282 - 289	142 - 149
1	9	SER	SER	ALA	ALA	A	A	292 - 301	152 - 161
2	9	SER	SER	ALA	ALA	B	B	292 - 301	152 - 161
1	10	GLY	GLY	ILE	ILE	A	A	309 - 319	169 - 179
2	10	GLY	GLY	ILE	ILE	B	B	309 - 319	169 - 179
1	11	ASP	ASP	ARG	ARG	A	A	321 - 333	181 - 193
2	11	ASP	ASP	ARG	ARG	B	B	321 - 333	181 - 193
1	12	PHE	PHE	SER	SER	A	A	345 - 354	205 - 214
2	12	PHE	PHE	SER	SER	B	B	345 - 354	205 - 214
1	13	ALA	ALA	LEU	LEU	A	A	365 - 407	225 - 267
2	13	ALA	ALA	LEU	LEU	B	B	365 - 407	225 - 267
1	14	ALA	ALA	HIS	HIS	A	A	413 - 452	273 - 312
2	14	ALA	ALA	HIS	HIS	B	B	413 - 452	273 - 312
1	15	LYS	LYS	ARG	ARG	A	A	460 - 481	320 - 341
2	15	LYS	LYS	ARG	ARG	B	B	460 - 481	320 - 341
1	16	GLY	GLY	VAL	VAL	A	A	497 - 532	357 - 392
2	16	GLY	GLY	VAL	VAL	B	B	497 - 532	357 - 392

#1: Protein	Protein Rv1364c/MT1410 Mass: 42323.625 Da / Num. of mol.: 2 / Fragment: UNP residues 169-539 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): Rosetta(DE3)pLysS / References: UniProt: Q11034, UniProt: P9WLZ7*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.02 %
Crystal grow	Temperature: 292.16 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.2 M ammonium sulphate, 0.05 M N-(2-Acetamido)iminodiacetic Acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.16K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2006
Radiation	Monochromator: Double crystal Si[111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→20 Å / Num. all: 27047 / Num. obs: 27047 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.2 % / B_iso Wilson estimate: 62.5 Å² / R_merge(I) obs: 0.118 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 2.67 / Num. unique all: 1291 / % possible all: 98

-
Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→19.63 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.909 / SU B: 20.515 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26681	1356	5 %	RANDOM
R_work	0.2081	-	-	-
all	0.21096	25612	-	-
obs	0.21096	25612	99.2 %	-

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: 44.941 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.46 Å²	0 Å²	0 Å²
2-	-	1.46 Å²	0 Å²
3-	-	-	-2.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→19.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5169	0	15	103	5287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	5311
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3415
X-RAY DIFFRACTION	r_angle_refined_deg	1.383	1.96	7213
X-RAY DIFFRACTION	r_angle_other_deg	0.907	3	8314
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.701	5	700
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.592	23.116	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.992	15	787
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.807	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	855
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6022
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1068
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1170
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	3507
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	2584
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	3013
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	196
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.192	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.017	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.812	1.5	4446
X-RAY DIFFRACTION	r_mcbond_other	0.104	1.5	1437
X-RAY DIFFRACTION	r_mcangle_it	1.063	2.5	5558
X-RAY DIFFRACTION	r_scbond_it	2.949	5	2011
X-RAY DIFFRACTION	r_scangle_it	4.22	10	1654

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3439 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.47	0.5
medium thermal	0.58	2.5

LS refinement shell

Resolution: 2.6→2.666 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	94	-
R_work	0.268	1787	-
obs	-	1787	96.76 %

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	4.0596	1.7042	1.0176	6.4496	-0.5576	1.4272	-0.1813	0.2599	0.05	-0.2196	0.0363	-0.8387	-0.1701	0.5885	0.1451	-0.3051	-0.0564	0.0646	0.0085	0.0718	0.0587	80.894	14.866	7.642
2	6.9972	2.6607	3.6051	3.1423	0.6834	2.2121	0.4791	-0.5093	-0.7107	0.6606	-0.3175	-1.1979	0.3859	0.2237	-0.1616	-0.1533	0.0427	-0.1349	0.0664	0.0621	0.3354	84.206	2.819	17.544
3	4.3629	1.4817	-0.6737	4.114	-0.7898	6.2591	-0.2402	0.0956	-0.3082	-0.0501	0.0832	0.2181	0.4738	-0.6133	0.1571	-0.3225	-0.0433	-0.0121	-0.3027	-0.0433	-0.336	48.334	-2.757	11.41
4	13.2453	2.2887	9.0761	3.3045	1.8545	8.4487	-0.2721	-1.1559	0.9407	0.1703	-0.2945	0.4295	-0.5178	-0.7804	0.5666	-0.2177	0.0153	0.0052	-0.1604	-0.024	-0.242	50.072	7.283	10.285
5	6.0638	-1.869	0.5836	4.3615	-0.4138	2.8878	-0.029	0.0676	-0.0334	0.1986	0.2933	0.7921	-0.3026	-0.8355	-0.2643	-0.2989	0.0615	0.0799	-0.0012	0.1433	0.0832	17.038	7.902	34.844
6	6.5011	-1.9743	3.1981	2.0155	-1.2466	3.5474	0.5643	0.7657	-1.1492	-0.5495	-0.0364	1.0996	0.9169	-0.6333	-0.5279	-0.0799	-0.123	-0.2096	0.1984	-0.051	0.4355	16.697	-5.008	24.937
7	4.2112	-1.0635	-0.9486	3.4607	0.2779	6.2664	-0.0958	0.0322	-0.2053	-0.081	-0.0728	-0.2454	0.2819	0.6127	0.1686	-0.3371	0.056	-0.0085	-0.318	0.027	-0.3323	52.655	-2.363	31.761
8	11.3269	-0.3834	8.1224	3.0625	0.3115	10.8522	-0.188	0.8642	0.8718	-0.1248	-0.13	-0.2315	-0.5724	0.4623	0.318	-0.2074	-0.0107	0.0144	-0.2816	0.0834	-0.2908	48.819	6.923	32.847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 325
2	X-RAY DIFFRACTION	2	A	326 - 403
3	X-RAY DIFFRACTION	3	A	404 - 474
4	X-RAY DIFFRACTION	4	A	475 - 532
5	X-RAY DIFFRACTION	5	B	16 - 325
6	X-RAY DIFFRACTION	6	B	326 - 403
7	X-RAY DIFFRACTION	7	B	404 - 474
8	X-RAY DIFFRACTION	8	B	475 - 532

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi