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- PDB-1jln: Crystal structure of the catalytic domain of protein tyrosine pho... -

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Basic information

Entry
Database: PDB / ID: 1jln
TitleCrystal structure of the catalytic domain of protein tyrosine phosphatase PTP-SL/BR7
ComponentsProtein Tyrosine Phosphatase, receptor type, R
KeywordsHYDROLASE / protein tyrosine phosphatase / PTP-SL / PTPBR7 / ERK2-MAP kinase regulation
Function / homology
Function and homology information


negative regulation of epithelial cell migration / ERBB2 signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of ERK1 and ERK2 cascade / cell junction / in utero embryonic development / protein kinase binding / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase R
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSzedlacsek, S.E. / Aricescu, A.R. / Fulga, T.A. / Renault, L. / Scheidig, A.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of PTP-SL/PTPBR7 catalytic domain: implications for MAP kinase regulation.
Authors: Szedlacsek, S.E. / Aricescu, A.R. / Fulga, T.A. / Renault, L. / Scheidig, A.J.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Tyrosine Phosphatase, receptor type, R


Theoretical massNumber of molelcules
Total (without water)33,7461
Polymers33,7461
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.136, 65.322, 105.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Protein Tyrosine Phosphatase, receptor type, R / E.C.3.1.3.48 / STEP-like PTPase / protein-tyrosine-phosphatase receptor type PTPBR7 / PTPBR7


Mass: 33745.637 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q62132, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG33501reservoir
2100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 26, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→19.69 Å / Num. all: 26218 / Num. obs: 24970 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 5.7 / Net I/σ(I): 17.1
Reflection shellResolution: 1.81→1.9 Å / Mean I/σ(I) obs: 2.62 / % possible all: 40.3
Reflection
*PLUS
Num. measured all: 118144

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
X-GENdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFO

1yfo


Resolution: 1.81→19.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 197719.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1248 5 %RANDOM
Rwork0.195 ---
all0.195 26218 --
obs0.195 24970 83.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4434 Å2 / ksol: 0.32837 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20 Å2
2--0.21 Å20 Å2
3---2.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.81→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 0 238 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it5.312
X-RAY DIFFRACTIONc_scbond_it5.122
X-RAY DIFFRACTIONc_scangle_it7.432.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 111 5 %
Rwork0.24 2108 -
obs--44.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / % reflection Rfree: 5 % / Rfactor Rwork: 0.24

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