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- PDB-1u2q: Crystal structure of Mycobacterium tuberculosis Low Molecular Wei... -

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Basic information

Entry
Database: PDB / ID: 1u2q
TitleCrystal structure of Mycobacterium tuberculosis Low Molecular Weight Protein Tyrosine Phosphatase (MPtpA) at 2.5A resolution with glycerol in the active site
Componentslow molecular weight protein-tyrosine-phosphatase
KeywordsHYDROLASE / tyrosine phosphatase / mycobacterium tuberculosis
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell endomembrane system / symbiont-mediated perturbation of host phagocytosis / : / Blockage of phagosome acidification / symbiont-mediated suppression of host apoptosis / Suppression of apoptosis / host cell cytoplasmic vesicle / Prevention of phagosomal-lysosomal fusion / protein dephosphorylation / protein-tyrosine-phosphatase ...symbiont-mediated perturbation of host cell endomembrane system / symbiont-mediated perturbation of host phagocytosis / : / Blockage of phagosome acidification / symbiont-mediated suppression of host apoptosis / Suppression of apoptosis / host cell cytoplasmic vesicle / Prevention of phagosomal-lysosomal fusion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Modulation by Mtb of host immune system / host cell nucleus / extracellular region / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Low molecular weight protein-tyrosine phosphatase A / Low molecular weight protein-tyrosine phosphatase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMadhurantakam, C. / Rajakumara, E. / Mazumdar, P.A. / Saha, B. / Mitra, D. / Wiker, H.G. / Sankaranarayanan, R. / Das, A.K.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal Structure of Low-Molecular-Weight Protein Tyrosine Phosphatase from Mycobacterium tuberculosis at 1.9-A Resolution
Authors: Madhurantakam, C. / Rajakumara, E. / Mazumdar, P.A. / Saha, B. / Mitra, D. / Wiker, H.G. / Sankaranarayanan, R. / Das, A.K.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: low molecular weight protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0473
Polymers17,9191
Non-polymers1282
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.311, 53.003, 64.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer and the asymmetric unit contains a monomer.

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Components

#1: Protein low molecular weight protein-tyrosine-phosphatase / PTPase


Mass: 17919.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MPTPA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009
References: UniProt: P65716, UniProt: P9WIA1*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, tri-sodium citrate dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2004 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 6167 / Num. obs: 5818 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 435 / Rsym value: 0.135 / % possible all: 71.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5PNT

5pnt


Resolution: 2.5→24.49 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 951668.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 301 5.2 %RANDOM
Rwork0.212 ---
all0.216 5833 --
obs0.212 5818 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3568 Å2 / ksol: 0.366337 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-10.58 Å20 Å20 Å2
2---3.53 Å20 Å2
3----7.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 7 83 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.101 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.44 19 4.2 %
Rwork0.264 431 -
obs-460 75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCNS_ION.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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