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- PDB-2hc2: Engineered protein tyrosine phosphatase beta catalytic domain -

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Basic information

Entry
Database: PDB / ID: 2hc2
TitleEngineered protein tyrosine phosphatase beta catalytic domain
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
Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 15, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)33,8514
Polymers33,7801
Non-polymers703
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.314, 70.775, 49.846
Angle α, β, γ (deg.)90.000, 92.520, 90.000
Int Tables number4
Space group name H-MP1211

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 38.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.85
Details: 21% PEG 8000, 200 mM MgCl2, 1% BME, 0.1% BOG, 1mM DTT, 80 mM Na Citrate, pH 7.85, 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: Feb 2, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.67 Å / Num. all: 48397 / Num. obs: 48397 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 20.2
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.87 / % possible all: 69.4

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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: 2HC1

2hc1


Resolution: 1.4→33.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.945 / SU ML: 0.035 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17892 2464 5.1 %RANDOM
Rwork0.14391 ---
obs0.14571 45933 92.51 %-
all-48397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.05 Å2
2---0.32 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 3 303 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9473537
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8965342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76723.577137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77515474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5821524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21757
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0241.51511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.13822495
X-RAY DIFFRACTIONr_scbond_it5.30831105
X-RAY DIFFRACTIONr_scangle_it6.9594.51009
X-RAY DIFFRACTIONr_rigid_bond_restr3.48732616
X-RAY DIFFRACTIONr_sphericity_free16.3733306
X-RAY DIFFRACTIONr_sphericity_bonded10.46532488
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 121 -
Rwork0.155 2286 -
obs--62.23 %

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