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- PDB-1txo: Crystal structure of the Mycobacterium tuberculosis serine/threon... -

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Basic information

Entry
Database: PDB / ID: 1txo
TitleCrystal structure of the Mycobacterium tuberculosis serine/threonine phosphatase PstP/Ppp at 1.95 A.
ComponentsPutative Bacterial Enzyme
KeywordsHYDROLASE / Putative Bacterial Enzyme / Serine/threonine protein phosphatases / PstP/Ppp / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


negative regulation of catalytic activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of catalytic activity / negative regulation of DNA binding / phosphoprotein phosphatase activity / protein dephosphorylation / peptidoglycan-based cell wall / negative regulation of protein kinase activity ...negative regulation of catalytic activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of catalytic activity / negative regulation of DNA binding / phosphoprotein phosphatase activity / protein dephosphorylation / peptidoglycan-based cell wall / negative regulation of protein kinase activity / manganese ion binding / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein phosphatase 2C / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine protein phosphatase PstP / Serine/threonine protein phosphatase PstP
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsPullen, K.E. / Ng, H.L. / Sung, P.Y. / Good, M.C. / Smith, S.M. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2004
Title: An Alternate Conformation and a Third Metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr Protein Phosphatase.
Authors: Pullen, K.E. / Ng, H.L. / Sung, P.Y. / Good, M.C. / Smith, S.M. / Alber, T.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Sep 21, 2016Group: Other
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Bacterial Enzyme
B: Putative Bacterial Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2978
Polymers50,9672
Non-polymers3306
Water4,342241
1
A: Putative Bacterial Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6484
Polymers25,4841
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Bacterial Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6484
Polymers25,4841
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.638, 58.757, 73.815
Angle α, β, γ (deg.)90.00, 102.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative Bacterial Enzyme / Serine/threonine protein phosphatases / PstP/Ppp


Mass: 25483.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)
References: UniProt: Q8VKT2, UniProt: P9WHW5*PLUS, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 10,000, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12714, 0.97960, 0.95373, 1.8926
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2003
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.127141
20.97961
30.953731
41.89261
ReflectionResolution: 1.95→72.55 Å / Num. all: 41602 / Num. obs: 38658 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.06 / Net I/σ(I): 18.3
Reflection shellHighest resolution: 1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1.9 / Num. unique all: 41602 / Rsym value: 0.415 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
ELVESdata reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→72.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.631 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23025 2042 5 %RANDOM
Rwork0.19904 ---
all0.225 41602 --
obs0.20057 38658 98.05 %-
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: 29.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.08 Å2
2--1.5 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 6 241 3701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213496
X-RAY DIFFRACTIONr_bond_other_d0.0020.023308
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.9764750
X-RAY DIFFRACTIONr_angle_other_deg0.72937608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.1810.2633
X-RAY DIFFRACTIONr_nbd_other0.2310.23722
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.22126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.52322
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18423682
X-RAY DIFFRACTIONr_scbond_it1.59631174
X-RAY DIFFRACTIONr_scangle_it2.7934.51068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 109
Rwork0.199 2507

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