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- PDB-7xc0: Crystal structure of Human RPTPH -

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Basic information

Entry
Database: PDB / ID: 7xc0
TitleCrystal structure of Human RPTPH
ComponentsReceptor-type tyrosine-protein phosphatase H
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / microvillus membrane / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nuclear speck / cadherin binding / apical plasma membrane / apoptotic process / plasma membrane / cytosol
Similarity search - Function
: / 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 ...: / 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
Similarity search - Domain/homology
PHOSPHATE ION / Receptor-type tyrosine-protein phosphatase H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKim, M. / Ryu, S.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of the catalytic domain of human RPTPH.
Authors: Kim, M. / Ryu, S.E.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3222
Polymers33,2281
Non-polymers951
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-6 kcal/mol
Surface area12880 Å2
Unit cell
Length a, b, c (Å)56.460, 56.460, 80.447
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase H / R-PTP-H / Stomach cancer-associated protein tyrosine phosphatase 1 / SAP-1 / Transmembrane-type ...R-PTP-H / Stomach cancer-associated protein tyrosine phosphatase 1 / SAP-1 / Transmembrane-type protein-tyrosine phosphatase type H


Mass: 33227.508 Da / Num. of mol.: 1 / Mutation: C818A, C1020S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRH, SAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD43, protein-tyrosine-phosphatase
#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.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES-NaOH pH 6.5, 13%(v/v) PEGMME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.56→24.45 Å / Num. obs: 38471 / % possible obs: 94.23 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0694 / Net I/σ(I): 10.6
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3167 / Mean I/σ(I) obs: 2.89 / Num. unique obs: 3574 / CC1/2: 0.389 / % possible all: 87.66

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NZ6

2nz6


Resolution: 1.56→24.45 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 27.1523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 1980 5.14 %
Rwork0.1781 36550 -
obs0.1796 38471 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 1.56→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 5 189 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272388
X-RAY DIFFRACTIONf_angle_d0.59883251
X-RAY DIFFRACTIONf_chiral_restr0.0426344
X-RAY DIFFRACTIONf_plane_restr0.0044426
X-RAY DIFFRACTIONf_dihedral_angle_d5.5456313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.31131250.29272371X-RAY DIFFRACTION86.64
1.6-1.640.31291240.27512468X-RAY DIFFRACTION87.6
1.64-1.690.28881410.24782475X-RAY DIFFRACTION89.62
1.69-1.740.2731340.22612471X-RAY DIFFRACTION90.58
1.74-1.810.22171350.22362613X-RAY DIFFRACTION92.99
1.81-1.880.24031330.18862617X-RAY DIFFRACTION93.57
1.88-1.960.22231450.17252629X-RAY DIFFRACTION95.07
1.96-2.070.20121470.21212671X-RAY DIFFRACTION96.21
2.07-2.20.21571570.20252671X-RAY DIFFRACTION97.52
2.2-2.370.21241490.18982723X-RAY DIFFRACTION98.22
2.37-2.60.20251530.192745X-RAY DIFFRACTION98.77
2.6-2.980.19021400.18112796X-RAY DIFFRACTION99.16
2.98-3.750.20181540.15652741X-RAY DIFFRACTION99.48
3.75-24.450.18471430.14442559X-RAY DIFFRACTION92.72

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