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- PDB-2i3u: Structural studies of protein tyrosine phosphatase beta catalytic... -

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Basic information

Entry
Database: PDB / ID: 2i3u
TitleStructural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors
ComponentsReceptor-type tyrosine-protein phosphatase beta
KeywordsHYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.
Authors: Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. / Cox, B. / Li, C. / Bechard, R. / Genbauffe, F. / Andrews, R. / Diven, C. / Howard, B. / Rastogi, V. / Gray, J. / Maier, M. / Peters, K.G.
History
DepositionAug 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase beta


Theoretical massNumber of molelcules
Total (without water)36,2881
Polymers36,2881
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.785, 69.777, 118.523
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 Receptor-type tyrosine-protein phosphatase beta / Protein-tyrosine phosphatase beta / R-PTP-beta


Mass: 36288.035 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1662-1973
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2004 / Details: Si monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→22.31 Å / Num. all: 27971 / Num. obs: 27971 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 21.75
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.11 / Num. unique all: 3939 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I3R

2i3r


Resolution: 1.85→22.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.312 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1409 5 %RANDOM
Rwork0.187 ---
obs0.187 27925 98.34 %-
all-27925 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.85→22.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 0 204 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212393
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9423263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9835298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60123.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70315417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7161522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021856
X-RAY DIFFRACTIONr_nbd_refined0.2540.21133
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.560.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.224
X-RAY DIFFRACTIONr_mcbond_it2.3871.51461
X-RAY DIFFRACTIONr_mcangle_it3.22522315
X-RAY DIFFRACTIONr_scbond_it4.78331067
X-RAY DIFFRACTIONr_scangle_it6.814.5936
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 101 -
Rwork0.216 1726 -
obs-1827 89.17 %
Refinement TLS params.Method: refined / Details: Chain A / Origin x: 1.907 Å / Origin y: 21.749 Å / Origin z: 14.919 Å
111213212223313233
T-0.0439 Å2-0.0144 Å20.0016 Å2--0.0406 Å20.0061 Å2---0.0439 Å2
L0.2665 °2-0.0601 °2-0.0149 °2-0.207 °2-0.0927 °2--0.5541 °2
S-0.032 Å °0.0225 Å °0.0227 Å °0.0298 Å °0.0044 Å °0.0044 Å °-0.0446 Å °0.0251 Å °0.0275 Å °
Refinement TLS groupSelection: ALL

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