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- PDB-3o4s: Crystal Structure of HePTP with a Closed WPD Loop and an Ordered ... -

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Basic information

Entry
Database: PDB / ID: 3o4s
TitleCrystal Structure of HePTP with a Closed WPD Loop and an Ordered E-Loop
ComponentsTyrosine-protein phosphatase non-receptor type 7
KeywordsHYDROLASE / HEPTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7
Function / homology
Function and homology information


Interleukin-37 signaling / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / mitotic spindle ...Interleukin-37 signaling / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / mitotic spindle / MAPK cascade / microtubule cytoskeleton / signal transduction / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
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, 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsCritton, D.A. / Page, R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Visualizing active-site dynamics in single crystals of HePTP: opening of the WPD loop involves coordinated movement of the E loop.
Authors: Critton, D.A. / Tautz, L. / Page, R.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,27012
Polymers35,2331
Non-polymers1,03711
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.795, 39.130, 83.441
Angle α, β, γ (deg.)90.00, 124.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 35232.801 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 65-360 / Mutation: S72D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 23, 2009 / Details: OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(III) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25307 / Num. obs: 25241 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.092 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1246 / Rsym value: 0.512 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2QDM

2qdm


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.98 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES AND SIDECHAINS FOR WHICH NO DENSITY WAS OBSERVED WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.21214 1287 5.1 %RANDOM
Rwork0.1617 ---
obs0.16425 23923 99.59 %-
all-23923 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.059 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20.99 Å2
2---0.32 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 60 277 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222449
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9763324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8724.138116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68815405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8591517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021855
X-RAY DIFFRACTIONr_nbd_refined0.2090.21193
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.233
X-RAY DIFFRACTIONr_mcbond_it1.70531522
X-RAY DIFFRACTIONr_mcangle_it2.55752384
X-RAY DIFFRACTIONr_scbond_it4.19481060
X-RAY DIFFRACTIONr_scangle_it5.91411940
LS refinement shellResolution: 1.9→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 84 -
Rwork0.213 1744 -
obs--97.65 %

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