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- PDB-2oz5: Crystal structure of Mycobacterium tuberculosis protein tyrosine ... -

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Basic information

Entry
Database: PDB / ID: 2oz5
TitleCrystal structure of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB in complex with the specific inhibitor OMTS
ComponentsPhosphotyrosine protein phosphatase ptpbTyrosine
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein tyrosine phosphatase in complex with small molecule inhibitor / 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
Chem-7XY / : / Tyrosine specific protein phosphatases domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrundner, C. / Gee, C.L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2007
Title: Structural Basis for Selective Inhibition of Mycobacterium tuberculosis Protein Tyrosine Phosphatase PtpB.
Authors: Grundner, C. / Perrin, D. / Hooft van Huijsduijnen, R. / Swinnen, D. / Gonzalez, J. / Gee, C.L. / Wells, T.N. / Alber, T.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
B: Phosphotyrosine protein phosphatase ptpb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0636
Polymers64,7302
Non-polymers2,3324
Water6,485360
1
A: Phosphotyrosine protein phosphatase ptpb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5313
Polymers32,3651
Non-polymers1,1662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphotyrosine protein phosphatase ptpb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5313
Polymers32,3651
Non-polymers1,1662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.396, 72.488, 96.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphotyrosine protein phosphatase ptpb / Tyrosine


Mass: 32365.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ptpB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: A1QMT0, UniProt: P96830*PLUS
#2: Chemical
ChemComp-7XY / {(3-CHLOROBENZYL)[(5-{[(3,3-DIPHENYLPROPYL)AMINO]SULFONYL}-2-THIENYL)METHYL]AMINO}(OXO)ACETIC ACID


Mass: 583.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H27ClN2O5S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium acetate, 0.1M Bis-Tris pH5.5 17% PEG 10,000 0.5% beta-octylgucoside, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2006
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34740 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Χ2: 0.814 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.071.90.0928390.706180.8
2.07-2.152.20.07632580.711193
2.15-2.2530.0734530.828197.4
2.25-2.373.70.06434910.87199.4
2.37-2.524.20.06435581.0291100
2.52-2.714.20.0535400.8681100
2.71-2.994.20.03935720.7861100
2.99-3.424.20.03135860.7911100
3.42-4.314.20.02436330.7451100
4.31-5040.02138020.6671100

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Phasing

Phasing MRRfactor: 0.46 / Cor.coef. Fo:Fc: 0.472
Highest resolutionLowest resolution
Rotation3 Å48.03 Å
Translation3 Å48.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 3.98 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Some atoms in ARG 235 A, ARG 269 A, ARG 124 B, and ARG 258 B were modeled with zero occupancy leading to high RMS deviation values in these residues.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1789 5.1 %RANDOM
Rwork0.189 ---
obs0.192 34740 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 156 360 4550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224184
X-RAY DIFFRACTIONr_angle_refined_deg1.5112.0085683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9885521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1721.62179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90315628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3641555
X-RAY DIFFRACTIONr_chiral_restr0.0890.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023209
X-RAY DIFFRACTIONr_nbd_refined0.2020.22033
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.225
X-RAY DIFFRACTIONr_mcbond_it0.7371.52674
X-RAY DIFFRACTIONr_mcangle_it1.22524148
X-RAY DIFFRACTIONr_scbond_it2.05331696
X-RAY DIFFRACTIONr_scangle_it3.2174.51535
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 102 -
Rwork0.18 1965 -
obs-2067 79.56 %

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