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- PDB-3i36: Crystal Structure of Rat Protein Tyrosine Phosphatase eta Catalyt... -

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Basic information

Entry
Database: PDB / ID: 3i36
TitleCrystal Structure of Rat Protein Tyrosine Phosphatase eta Catalytic Domain
ComponentsVascular protein tyrosine phosphatase 1
KeywordsHYDROLASE / PTP / Tyrosine Phosphatase
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / negative regulation of vascular permeability / positive regulation of platelet activation / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / platelet formation / positive regulation of cell-matrix adhesion ...positive regulation of Fc receptor mediated stimulatory signaling pathway / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / negative regulation of vascular permeability / positive regulation of platelet activation / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / platelet formation / positive regulation of cell-matrix adhesion / negative regulation of T cell receptor signaling pathway / positive regulation of macrophage chemotaxis / positive chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / oligodendrocyte differentiation / phosphatase activity / positive regulation of focal adhesion assembly / platelet-derived growth factor receptor signaling pathway / immunological synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of cell adhesion / positive regulation of phagocytosis / negative regulation of insulin receptor signaling pathway / positive regulation of cell adhesion / protein-tyrosine-phosphatase / B cell differentiation / negative regulation of cell migration / protein tyrosine phosphatase activity / negative regulation of cell growth / beta-catenin binding / ruffle membrane / positive regulation of peptidyl-tyrosine phosphorylation / blood coagulation / positive regulation of tumor necrosis factor production / cell-cell junction / glucose homeostasis / heart development / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / cell surface / 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
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 Å
AuthorsNascimento, A.S. / Matozo, H.C. / Santos, M.A. / Polikarpov, I.
CitationJournal: To be Published
Title: To be Published
Authors: Nascimento, A.S. / Matozo, H.C. / Palmieri, D. / Iuliano, R. / Santos, M.A.M. / Fusco, A. / Polikarpov, I.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vascular protein tyrosine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9272
Polymers39,8911
Non-polymers351
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.468, 63.113, 111.655
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 Vascular protein tyrosine phosphatase 1


Mass: 39891.371 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (UNP residues 875 to 1216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ptprj / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62884, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 20% PEG 10000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.42
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.84→37.42 Å / Num. obs: 28395 / % possible obs: 97.6 % / Observed criterion σ(I): 2.9 / Redundancy: 3.5 % / Biso Wilson estimate: 21.014 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.1
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.238 / % possible all: 95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHS

2ahs


Resolution: 1.841→35.715 Å / SU ML: 1.5 / σ(F): 0.04 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1406 5.12 %
Rwork0.1569 --
obs0.1592 27482 94.16 %
all-54924 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.361 e/Å3
Refinement stepCycle: LAST / Resolution: 1.841→35.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 1 443 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092405
X-RAY DIFFRACTIONf_angle_d1.2373278
X-RAY DIFFRACTIONf_dihedral_angle_d15.971873
X-RAY DIFFRACTIONf_chiral_restr0.071357
X-RAY DIFFRACTIONf_plane_restr0.005425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.841-1.90680.24791260.19092299X-RAY DIFFRACTION85
1.9068-1.98310.22461470.16512449X-RAY DIFFRACTION91
1.9831-2.07340.19151240.162566X-RAY DIFFRACTION94
2.0734-2.18260.21461450.14952583X-RAY DIFFRACTION95
2.1826-2.31940.1931390.15362652X-RAY DIFFRACTION96
2.3194-2.49840.20521540.14972647X-RAY DIFFRACTION97
2.4984-2.74980.20781320.14592730X-RAY DIFFRACTION98
2.7498-3.14740.20461420.14522694X-RAY DIFFRACTION97
3.1474-3.96460.16791400.14012656X-RAY DIFFRACTION94
3.9646-35.72180.19261570.15462800X-RAY DIFFRACTION95
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.9222-0.1383-0.74431.65540.89751.40290.0395-0.05440.0073-0.30630.3985-0.4592-0.19510.4387-0.35520.1598-0.07410.05270.2516-0.12850.1578.9348-8.8164.9581
20.44280.20020.02320.3480.68710.45470.06950.1257-0.0874-0.05810.01610.0053-0.0817-0.0658-0.06340.1602-0.00850.0180.1285-0.03820.1323
3-0.0429-0.06040.06270.8931-0.0070.67650.0931-0.072-0.1529-0.036-0.11590.20640.1461-0.2151-0.00840.091-0.02880.00710.1342-0.00620.1399
4-0.39370.2786-0.21510.852-0.22031.11840.11610.03360.13810.0984-0.12830.34430.05-0.25920.00840.0834-0.03670.05860.1347-0.03050.1467
5-0.15060.0707-0.66370.6467-0.40040.2673-0.076-0.42480.02190.08260.02790.0889-0.071-0.02820.03210.07130.0027-0.00680.1411-0.02870.1022
61.21990.1619-0.61410.9780.14740.70.04760.12240.2121-0.0031-0.07050.2235-0.167-0.1560.00560.0960.0283-0.01540.1016-0.00030.1311
70.2915-0.02680.05310.0384-0.5073-0.05760.0483-0.09670.16210.1111-0.02740.0658-0.06560.2130.00540.1706-0.01910.00190.1153-0.0260.1748
80.4719-0.1748-0.20711.02920.9191.15330.0339-0.01040.1438-0.15350.0423-0.1571-0.1722-0.0582-0.09070.1047-0.01050.02640.07910.00920.1054
90.461-0.0722-0.2410.56770.37380.3387-0.04590.0154-0.07850.01450.0691-0.09840.01010.0318-0.01640.1016-0.0015-0.00340.0997-0.0140.107
101.4134-0.0072-0.58290.0929-0.34390.21840.11010.30550.0468-0.0141-0.04050.0526-0.2259-0.1405-0.06290.2493-0.03410.02080.1141-0.02020.0826
Refinement TLS groupSelection details: CHAIN A AND RESID 1162:1180)

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