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- PDB-1ywf: Crystal Structure of Mycobacterium Tuberculosis Protein Tyrosine ... -

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Basic information

Entry
Database: PDB / ID: 1ywf
TitleCrystal Structure of Mycobacterium Tuberculosis Protein Tyrosine Phosphatase PtpB
ComponentsPHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB
KeywordsUNKNOWN FUNCTION / Four stranded parallel beta sheet with flanking helices / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


phosphatidylinositol trisphosphate phosphatase activity / biological process involved in interaction with host / protein serine/threonine phosphatase activity / phosphatase activity / protein dephosphorylation / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
Tyrosine/serine-protein phosphatase IphP-type / Tyrosine phosphatase family / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine specific protein phosphatases domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.71 Å
AuthorsGrundner, C. / Ng, H.L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2005
Title: Mycobacterium tuberculosis Protein Tyrosine Phosphatase PtpB Structure Reveals a Diverged Fold and a Buried Active Site.
Authors: Grundner, C. / Ng, H.L. / Alber, T.
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4602
Polymers32,3651
Non-polymers951
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.068, 113.068, 53.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

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Components

#1: Protein PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB


Mass: 32365.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET28b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P96830
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.63 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05M KH2PO4, 20% PEG8000, 10mM NaAcetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1157, 0.97949, 0.97973, 0.93927
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2004
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11571
20.979491
30.979731
40.939271
ReflectionResolution: 1.7→79 Å / Num. all: 33939 / Num. obs: 33939 / % possible obs: 91.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.041 / Net I/σ(I): 66.7
Reflection shellResolution: 1.7→1.76 Å / % possible all: 48.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.71→79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.244 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21361 1692 5 %RANDOM
Rwork0.17567 ---
all0.17755 36301 --
obs0.17755 32240 93.47 %-
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: 28.706 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2---1.99 Å20 Å2
3---3.98 Å2
Refinement stepCycle: LAST / Resolution: 1.71→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 5 264 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211889
X-RAY DIFFRACTIONr_bond_other_d0.0020.021797
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9662561
X-RAY DIFFRACTIONr_angle_other_deg0.91534107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575239
X-RAY DIFFRACTIONr_chiral_restr0.0840.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022137
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02424
X-RAY DIFFRACTIONr_nbd_refined0.220.2444
X-RAY DIFFRACTIONr_nbd_other0.2510.22236
X-RAY DIFFRACTIONr_nbtor_other0.0870.21177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.211
X-RAY DIFFRACTIONr_mcbond_it0.9781.51194
X-RAY DIFFRACTIONr_mcangle_it1.78821910
X-RAY DIFFRACTIONr_scbond_it2.8053695
X-RAY DIFFRACTIONr_scangle_it4.7294.5651
LS refinement shellResolution: 1.714→1.758 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 89
Rwork0.267 1609

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