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- PDB-3kx0: Crystal Structure of the PAS domain of Rv1364c -

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Basic information

Entry
Database: PDB / ID: 3kx0
TitleCrystal Structure of the PAS domain of Rv1364c
ComponentsUncharacterized protein Rv1364c/MT1410
KeywordsSIGNALING PROTEIN / PAS domain / Rv1364c / Sensory domain / Mycobacteium tuberculosis / Small molecule binding domain
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 ...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 / 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 / PAS fold / STAS domain / Sigma factor PP2C-like phosphatases / STAS domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / STAS domain profile. ...Histidine kinase-like ATPase domain / Stage II sporulation protein E (SpoIIE) / PAS fold-4 / PAS fold / STAS domain / Sigma factor PP2C-like phosphatases / STAS domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / STAS domain profile. / PPM-type phosphatase-like domain superfamily / STAS domain / STAS domain superfamily / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Beta-Lactamase / PAS domain / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Multidomain regulatory protein Rv1364c / Multidomain regulatory protein Rv1364c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJaiswal, R.K. / Gopal, B.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c
Authors: Jaiswal, R.K. / Manjeera, G. / Gopal, B.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Uncharacterized protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1702
Polymers21,1101
Non-polymers601
Water905
1
X: Uncharacterized protein Rv1364c/MT1410
hetero molecules

X: Uncharacterized protein Rv1364c/MT1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3394
Polymers42,2192
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3890 Å2
ΔGint-21 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.609, 59.609, 173.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Uncharacterized protein Rv1364c/MT1410


Mass: 21109.510 Da / Num. of mol.: 1 / Fragment: UNP residues 1-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1364c / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q11034, UniProt: P9WLZ7*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 300 K / Method: under oil / pH: 8
Details: 2.5M ammonium sulphate, 5% Isopropanol, .1M tris-chloride, pH 8, Under oil, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.3→57.74 Å / Num. obs: 8811 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.1 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 5.2 / Num. unique all: 21601 / Rsym value: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.475 Å / SU ML: 0.38 / σ(F): 0.02 / σ(I): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 399 4.72 %RANDOM
Rwork0.2329 ---
obs0.2349 8445 96.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.471 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 57.628 Å2
Baniso -1Baniso -2Baniso -3
1-8.784 Å2-0 Å2-0 Å2
2--8.784 Å20 Å2
3----17.568 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 4 5 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071031
X-RAY DIFFRACTIONf_angle_d1.0781401
X-RAY DIFFRACTIONf_dihedral_angle_d20.273372
X-RAY DIFFRACTIONf_chiral_restr0.076148
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.63290.32521230.23362482X-RAY DIFFRACTION93
2.6329-3.3170.24211350.22822659X-RAY DIFFRACTION97
3.317-49.48660.26821410.2312905X-RAY DIFFRACTION99
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)
10.78590.5288-0.10180.830.04922.61020.1475-0.2030.1090.25590.23360.022-0.29980.1262-0.21180.43860.10780.02610.1334-0.00870.2998-28.53373.326722.8689
26.4253-2.1773-1.6574.92223.45592.40390.48021.15671.2559-1.5301-0.2674-0.4476-1.63980.3037-0.16290.4862-0.29870.1010.3813-0.12140.5495-18.472715.710815.798
34.93630.6137-3.44890.43471.05576.79520.65080.8331.0298-0.9028-0.026-0.8789-1.9395-0.1923-0.61430.7570.01110.11960.25380.07140.3976-27.5215.36077.9303
42.2265-0.9297-0.9720.29841.20051.50750.16980.45780.3541-0.09320.1802-0.1794-0.6396-0.3988-0.21070.45110.0130.07560.22520.01190.2593-28.4529.05689.4304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain X and resid 4:47)X4 - 47
2X-RAY DIFFRACTION2(chain X and resid 48:74)X48 - 74
3X-RAY DIFFRACTION3(chain X and resid 75:104)X75 - 104
4X-RAY DIFFRACTION4(chain X and resid 105:138)X105 - 138

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