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- PDB-7rin: Apo PTP1B by Native S-SAD at Room Temperature -

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Basic information

Entry
Database: PDB / ID: 7rin
TitleApo PTP1B by Native S-SAD at Room Temperature
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / Protein Tyrosine Phosphatase 1B
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / cytoplasmic side of endoplasmic reticulum membrane / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of JUN kinase activity / positive regulation of systemic arterial blood pressure / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to angiotensin / regulation of proteolysis / non-membrane spanning protein tyrosine phosphatase activity / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / growth hormone receptor signaling pathway via JAK-STAT / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cardiac muscle cell apoptotic process / endoplasmic reticulum unfolded protein response / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / ephrin receptor binding / Integrin signaling / protein-tyrosine-phosphatase / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / response to nutrient levels / Negative regulation of MET activity / insulin receptor binding / cellular response to nerve growth factor stimulus / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Hekstra, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privateSearle Scholars Program (SSP-2018-3240) United States
Other privateGeorge W. Merck Fund in the New York Community Trust (338034) United States
National Science Foundation (NSF, United States)DGE1745303 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Native SAD phasing at room temperature.
Authors: Greisman, J.B. / Dalton, K.M. / Sheehan, C.J. / Klureza, M.A. / Kurinov, I. / Hekstra, D.R.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5903
Polymers37,3461
Non-polymers2442
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.538, 89.538, 106.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 37345.562 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C32S,C92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.29 Å3/Da / Density % sol: 62.6 % / Description: Hexagonal rod
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES (pH 6.8 - 7.6), 250mM magnesium acetate, 11-15% PEG8000 (w/v), 10% glycerol (v/v), 6% ethanol (v/v), 0.1% BME (v/v).
PH range: 6.8 - 7.6

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.892 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 1.85→77.54 Å / Num. obs: 81017 / % possible obs: 99.68 % / Redundancy: 29.8 % / Biso Wilson estimate: 29.56 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1425 / Rpim(I) all: 0.02393 / Rrim(I) all: 0.1446 / Net I/σ(I): 15.29
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.466 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 7932 / CC1/2: 0.61 / CC star: 0.87 / Rpim(I) all: 0.3981 / Rrim(I) all: 1.522 / % possible all: 97.3

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Processing

Software
NameVersionClassification
DIALS3.2.0data reduction
Aimless0.7.4data scaling
AutoSol1.18.2_3874phasing
PHENIX1.18.2_3874model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 1.85→77.54 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.8988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1538 4067 5.02 %
Rwork0.1318 76948 -
obs0.1329 81015 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.45 Å2
Refinement stepCycle: LAST / Resolution: 1.85→77.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 16 159 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982950
X-RAY DIFFRACTIONf_angle_d1.01814011
X-RAY DIFFRACTIONf_chiral_restr0.062411
X-RAY DIFFRACTIONf_plane_restr0.007529
X-RAY DIFFRACTIONf_dihedral_angle_d15.93321145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.31011350.27972543X-RAY DIFFRACTION96.09
1.87-1.890.23581780.24562570X-RAY DIFFRACTION97.21
1.89-1.920.24271360.22892603X-RAY DIFFRACTION98.67
1.92-1.940.22331340.2062661X-RAY DIFFRACTION99.15
1.94-1.970.1834900.18522653X-RAY DIFFRACTION99.64
1.97-20.19981580.1812707X-RAY DIFFRACTION100
2-2.030.16151700.15592594X-RAY DIFFRACTION100
2.03-2.060.18681420.14752675X-RAY DIFFRACTION100
2.06-2.090.17931740.13962635X-RAY DIFFRACTION100
2.09-2.130.16361380.13372677X-RAY DIFFRACTION100
2.13-2.170.15981340.1252673X-RAY DIFFRACTION100
2.17-2.210.12371700.12632622X-RAY DIFFRACTION100
2.21-2.260.14951160.11762694X-RAY DIFFRACTION100
2.26-2.30.15441860.11592601X-RAY DIFFRACTION100
2.3-2.360.12711420.11492693X-RAY DIFFRACTION100
2.36-2.420.13331500.11152619X-RAY DIFFRACTION100
2.42-2.480.1491980.11232731X-RAY DIFFRACTION100
2.48-2.560.14211040.112682X-RAY DIFFRACTION100
2.56-2.640.131100.12082663X-RAY DIFFRACTION100
2.64-2.730.12741500.11812692X-RAY DIFFRACTION100
2.73-2.840.14391280.11932633X-RAY DIFFRACTION100
2.84-2.970.15441400.12322674X-RAY DIFFRACTION100
2.97-3.130.17261540.1382634X-RAY DIFFRACTION100
3.13-3.320.16431460.13352694X-RAY DIFFRACTION100
3.32-3.580.1371440.1192661X-RAY DIFFRACTION100
3.58-3.940.10971600.11362625X-RAY DIFFRACTION100
3.94-4.510.11761340.10632667X-RAY DIFFRACTION100
4.51-5.680.14331020.11642695X-RAY DIFFRACTION100
5.69-77.540.22631440.18172677X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.47264633597 Å / Origin y: 47.7905718255 Å / Origin z: 50.9903975777 Å
111213212223313233
T0.193198017147 Å2-0.0598047657043 Å20.00213078092081 Å2-0.173314381768 Å20.0157713025863 Å2--0.1415191562 Å2
L1.00674194939 °20.36657342368 °20.0653598730437 °2-1.83001030884 °2-0.280036757902 °2--1.15868946426 °2
S0.0403403654761 Å °-0.0393912020723 Å °-0.00539372813851 Å °-0.0545082713218 Å °-0.0546642234439 Å °-0.0302928111532 Å °0.0774598033832 Å °0.153065474657 Å °0.00518027112788 Å °
Refinement TLS groupSelection details: all

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