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- PDB-2hc1: Engineered catalytic domain of protein tyrosine phosphatase HPTPbeta. -

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Basic information

Entry
Database: PDB / ID: 2hc1
TitleEngineered catalytic domain of protein tyrosine phosphatase HPTPbeta.
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 / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / angiogenesis ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / 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 profile. / Tyrosine-specific protein phosphatases domain / 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
ACETATE ION / Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEvdokimov, A.G. / Pokross, M. / Walter, R. / 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
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9104
Polymers33,7801
Non-polymers1303
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.060, 70.714, 118.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 33780.340 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB / Plasmid: pHisMBP-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 20% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, 180 mM Nh4OAc, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→33.88 Å / Num. all: 59896 / Num. obs: 59896 / % possible obs: 72.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.32
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.85 / % possible all: 69.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H02

2h02


Resolution: 1.3→33.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.4 / SU ML: 0.027 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17885 2998 5 %RANDOM
Rwork0.13376 ---
obs0.136 56897 72.63 %-
all-59895 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 6 362 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222735
X-RAY DIFFRACTIONr_bond_other_d0.0010.022454
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.953770
X-RAY DIFFRACTIONr_angle_other_deg0.735777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8765374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65723.691149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7911526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
X-RAY DIFFRACTIONr_nbd_refined0.250.2564
X-RAY DIFFRACTIONr_nbd_other0.240.22596
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21320
X-RAY DIFFRACTIONr_nbtor_other0.090.21516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3240.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0680.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8371.52136
X-RAY DIFFRACTIONr_mcbond_other1.2241.5640
X-RAY DIFFRACTIONr_mcangle_it3.29122650
X-RAY DIFFRACTIONr_scbond_it4.72731323
X-RAY DIFFRACTIONr_scangle_it5.8094.51078
X-RAY DIFFRACTIONr_rigid_bond_restr2.46136342
X-RAY DIFFRACTIONr_sphericity_free14.4313364
X-RAY DIFFRACTIONr_sphericity_bonded5.57435087
LS refinement shellResolution: 1.295→1.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 174 -
Rwork0.201 3437 -
obs--59.74 %

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