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- PDB-3k3d: The N-terminal PAS domain crystal structure of RV1364C from Mycob... -

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Basic information

Entry
Database: PDB / ID: 3k3d
TitleThe N-terminal PAS domain crystal structure of RV1364C from Mycobacterium Tuberculosis at 2.3 angstrom
ComponentsProtein Rv1364c/MT1410
KeywordsSIGNALING PROTEIN / SENSOR / PAS / SIGNAL TRANSDUCTION / FATTY-ACID BINDING / SIGMA FACTOR REGULATOR
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
Multidomain regulatory protein Rv1364c / Multidomain regulatory protein Rv1364c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKing-Scott, J. / Panjikar, S. / Tucker, P.A.
CitationJournal: To be Published
Title: The N-Terminal Pas Domain Crystal Structure of Rv1364C from Mycobacterium Tuberculosis at 2.3 Angstrom.
Authors: King-Scott, J. / Panjikar, S. / Tucker, P.A.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 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_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Rv1364c/MT1410


Theoretical massNumber of molelcules
Total (without water)16,8421
Polymers16,8421
Non-polymers00
Water36020
1
A: Protein Rv1364c/MT1410

A: Protein Rv1364c/MT1410


Theoretical massNumber of molelcules
Total (without water)33,6852
Polymers33,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area3400 Å2
ΔGint-20 kcal/mol
Surface area13500 Å2
MethodPISA
2
A: Protein Rv1364c/MT1410

A: Protein Rv1364c/MT1410

A: Protein Rv1364c/MT1410

A: Protein Rv1364c/MT1410


Theoretical massNumber of molelcules
Total (without water)67,3694
Polymers67,3694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area9040 Å2
ΔGint-44 kcal/mol
Surface area24760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.137, 60.137, 171.948
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 Protein Rv1364c/MT1410


Mass: 16842.314 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-147
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): B834(DE3)PLYSS / References: UniProt: Q11034, UniProt: P9WLZ7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 292.16 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M AMMONIUM SULFATE, 0.1 M TRIS- HCL, 0.1 M SODIUM CHLORIDE, pH 8.00, 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: BW7A / Wavelength: 0.972 / Wavelength: 0.972 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2006
RadiationMonochromator: FIXED EXIT DOUBLE CRYSTAL SI [111], HORIZONTALLY FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 8731 / Num. obs: 8731 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21.3 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 39
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 22.8 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 4.62 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
Auto-Rickshawphasing
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL BUILT FROM SELENIUM MAD

Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.941 / SU ML: 0.191 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1226 14.1 %RANDOM
Rwork0.243 ---
all0.251 8685 --
obs0.251 8685 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.53 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å21.51 Å20 Å2
2--3.02 Å20 Å2
3----4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 20 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221055
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.951431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2155127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78622.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5215172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2191515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02838
X-RAY DIFFRACTIONr_nbd_refined0.20.2443
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2710
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.210
X-RAY DIFFRACTIONr_mcbond_it0.6331.5651
X-RAY DIFFRACTIONr_mcangle_it1.1132.51024
X-RAY DIFFRACTIONr_scbond_it2.9055456
X-RAY DIFFRACTIONr_scangle_it4.49110406
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 63 -
Rwork0.297 450 -
obs-450 84.38 %
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)
16.2808-1.69350.89538.9688-4.35058.52860.20810.31830.2766-0.6502-0.147-0.47230.04640.9353-0.0611-0.06920.29420.0313-0.2617-0.0382-0.326718.841126.358232.1842
22.8933-3.11370.08019.398-0.8186.1052-0.0087-0.3539-0.68380.52070.20581.96460.4058-1.7719-0.1971-0.04670.19130.00580.21750.10110.1176-0.751526.593242.6956
31.5438-1.16812.271916.7656-15.08718.745-0.0207-0.5117-0.17610.67380.47010.3127-0.3592-1.3259-0.4493-0.07460.2680.0123-0.06050.0145-0.26145.780228.029948.7249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 26
2X-RAY DIFFRACTION2A27 - 95
3X-RAY DIFFRACTION3A103 - 138

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