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

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Basic information

Entry
Database: PDB / ID: 3ke6
TitleThe crystal structure of the RsbU and RsbW domains of Rv1364c from Mycobacterium tuberculosis
ComponentsProtein Rv1364c/MT1410
KeywordsUNKNOWN FUNCTION / anti-sigma factor / anti-sigma factor antagonist / phosphatase / pp2c / serine kinase / ATPase
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 ...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 / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Histidine kinase-like ATPase domain / : / Stage II sporulation protein E (SpoIIE) / PAS fold-4 / STAS domain / PAS fold / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Histidine kinase/HSP90-like ATPase ...Histidine kinase-like ATPase domain / : / Stage II sporulation protein E (SpoIIE) / PAS fold-4 / STAS domain / PAS fold / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Histidine kinase/HSP90-like ATPase / PPM-type phosphatase domain profile. / STAS domain / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / STAS domain profile. / STAS domain / STAS domain superfamily / PAS-associated, C-terminal / PAC domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / PAS domain / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Multidomain regulatory protein Rv1364c / Multidomain regulatory protein Rv1364c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKing-Scott, J. / Panjikar, S. / Tucker, P.A.
CitationJournal: 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
DepositionOct 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Rv1364c/MT1410
B: Protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0558
Polymers84,6472
Non-polymers4086
Water1,856103
1
A: Protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6225
Polymers42,3241
Non-polymers2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4343
Polymers42,3241
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein Rv1364c/MT1410
hetero molecules

B: Protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0558
Polymers84,6472
Non-polymers4086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area2840 Å2
ΔGint-48 kcal/mol
Surface area28730 Å2
MethodPISA
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 number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA175 - 18535 - 45
21GLYGLYALAALABB175 - 18535 - 45
12GLYGLYGLYGLYAA193 - 20253 - 62
22GLYGLYGLYGLYBB193 - 20253 - 62
13ARGARGVALVALAA204 - 21264 - 72
23ARGARGVALVALBB204 - 21264 - 72
14GLUGLUALAALAAA218 - 23678 - 96
24GLUGLUALAALABB218 - 23678 - 96
15VALVALLYSLYSAA240 - 252100 - 112
25VALVALLYSLYSBB240 - 252100 - 112
16SERSERPHEPHEAA259 - 269119 - 129
26SERSERPHEPHEBB259 - 269119 - 129
17SERSERALAALAAA271 - 279131 - 139
27SERSERALAALABB271 - 279131 - 139
18PROPROALAALAAA282 - 289142 - 149
28PROPROALAALABB282 - 289142 - 149
19SERSERALAALAAA292 - 301152 - 161
29SERSERALAALABB292 - 301152 - 161
110GLYGLYILEILEAA309 - 319169 - 179
210GLYGLYILEILEBB309 - 319169 - 179
111ASPASPARGARGAA321 - 333181 - 193
211ASPASPARGARGBB321 - 333181 - 193
112PHEPHESERSERAA345 - 354205 - 214
212PHEPHESERSERBB345 - 354205 - 214
113ALAALALEULEUAA365 - 407225 - 267
213ALAALALEULEUBB365 - 407225 - 267
114ALAALAHISHISAA413 - 452273 - 312
214ALAALAHISHISBB413 - 452273 - 312
115LYSLYSARGARGAA460 - 481320 - 341
215LYSLYSARGARGBB460 - 481320 - 341
116GLYGLYVALVALAA497 - 532357 - 392
216GLYGLYVALVALBB497 - 532357 - 392

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Components

#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


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


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2006
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 2.67 / Num. unique all: 1291 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.63 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26681 1356 5 %RANDOM
Rwork0.2081 ---
all0.21096 25612 --
obs0.21096 25612 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.941 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 15 103 5287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215311
X-RAY DIFFRACTIONr_bond_other_d0.0010.023415
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.967213
X-RAY DIFFRACTIONr_angle_other_deg0.90738314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59223.116215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99215787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8071544
X-RAY DIFFRACTIONr_chiral_restr0.080.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021068
X-RAY DIFFRACTIONr_nbd_refined0.2120.21170
X-RAY DIFFRACTIONr_nbd_other0.2030.23507
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22584
X-RAY DIFFRACTIONr_nbtor_other0.0870.23013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0170.21
X-RAY DIFFRACTIONr_mcbond_it0.8121.54446
X-RAY DIFFRACTIONr_mcbond_other0.1041.51437
X-RAY DIFFRACTIONr_mcangle_it1.0632.55558
X-RAY DIFFRACTIONr_scbond_it2.94952011
X-RAY DIFFRACTIONr_scangle_it4.22101654
Refine LS restraints NCS

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

TypeRms dev position (Å)Weight position
medium positional0.470.5
medium thermal0.582.5
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 94 -
Rwork0.268 1787 -
obs-1787 96.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.05961.70421.01766.4496-0.55761.4272-0.18130.25990.05-0.21960.0363-0.8387-0.17010.58850.1451-0.3051-0.05640.06460.00850.07180.058780.89414.8667.642
26.99722.66073.60513.14230.68342.21210.4791-0.5093-0.71070.6606-0.3175-1.19790.38590.2237-0.1616-0.15330.0427-0.13490.06640.06210.335484.2062.81917.544
34.36291.4817-0.67374.114-0.78986.2591-0.24020.0956-0.3082-0.05010.08320.21810.4738-0.61330.1571-0.3225-0.0433-0.0121-0.3027-0.0433-0.33648.334-2.75711.41
413.24532.28879.07613.30451.85458.4487-0.2721-1.15590.94070.1703-0.29450.4295-0.5178-0.78040.5666-0.21770.01530.0052-0.1604-0.024-0.24250.0727.28310.285
56.0638-1.8690.58364.3615-0.41382.8878-0.0290.0676-0.03340.19860.29330.7921-0.3026-0.8355-0.2643-0.29890.06150.0799-0.00120.14330.083217.0387.90234.844
66.5011-1.97433.19812.0155-1.24663.54740.56430.7657-1.1492-0.5495-0.03641.09960.9169-0.6333-0.5279-0.0799-0.123-0.20960.1984-0.0510.435516.697-5.00824.937
74.2112-1.0635-0.94863.46070.27796.2664-0.09580.0322-0.2053-0.081-0.0728-0.24540.28190.61270.1686-0.33710.056-0.0085-0.3180.027-0.332352.655-2.36331.761
811.3269-0.38348.12243.06250.311510.8522-0.1880.86420.8718-0.1248-0.13-0.2315-0.57240.46230.318-0.2074-0.01070.0144-0.28160.0834-0.290848.8196.92332.847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 325
2X-RAY DIFFRACTION2A326 - 403
3X-RAY DIFFRACTION3A404 - 474
4X-RAY DIFFRACTION4A475 - 532
5X-RAY DIFFRACTION5B16 - 325
6X-RAY DIFFRACTION6B326 - 403
7X-RAY DIFFRACTION7B404 - 474
8X-RAY DIFFRACTION8B475 - 532

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