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- PDB-4ikc: Crystal Structure of catalytic domain of PTPRQ -

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Basic information

Entry
Database: PDB / ID: 4ikc
TitleCrystal Structure of catalytic domain of PTPRQ
ComponentsPhosphotidylinositol phosphatase PTPRQ
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate 3-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / stereocilium base / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / detection of mechanical stimulus involved in sensory perception of sound / regulation of fat cell differentiation ...phosphatidylinositol-3,5-bisphosphate 3-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / stereocilium base / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / detection of mechanical stimulus involved in sensory perception of sound / regulation of fat cell differentiation / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / basal plasma membrane / receptor complex / apical plasma membrane
Similarity search - Function
: / 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 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
Phosphatidylinositol phosphatase PTPRQ
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYu, K.R. / Ryu, S.E. / Kim, S.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis for the dephosphorylating activity of PTPRQ towards phosphatidylinositide substrates
Authors: Yu, K.R. / Kim, Y.J. / Jung, S.K. / Ku, B. / Park, H. / Cho, S.Y. / Jung, H. / Chung, S.J. / Bae, K.H. / Lee, S.C. / Kim, B.Y. / Erikson, R.L. / Ryu, S.E. / Kim, S.J.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Nov 8, 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: Phosphotidylinositol phosphatase PTPRQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4743
Polymers32,3421
Non-polymers1322
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphotidylinositol phosphatase PTPRQ
hetero molecules

A: Phosphotidylinositol phosphatase PTPRQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9476
Polymers64,6842
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3150 Å2
ΔGint-78 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 77.580, 85.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-3250-

HOH

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Components

#1: Protein Phosphotidylinositol phosphatase PTPRQ / Receptor-type tyrosine-protein phosphatase Q / PTP-RQ / R-PTP-Q


Mass: 32342.002 Da / Num. of mol.: 1 / Fragment: UNP residues 2015-2254 / Mutation: C2879S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMZ3, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate, 0.2M magnesium acetate, 30% PEG4K, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→40 Å / Num. all: 41391 / Num. obs: 41238 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.56→1.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJT

2gjt


Resolution: 1.56→25.394 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 14.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 2057 5 %random
Rwork0.1474 ---
obs0.1483 41104 99.26 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.461 Å2 / ksol: 0.461 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1631 Å20 Å20 Å2
2---1.1631 Å20 Å2
3---2.3262 Å2
Refinement stepCycle: LAST / Resolution: 1.56→25.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 6 284 2498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132269
X-RAY DIFFRACTIONf_angle_d1.4643086
X-RAY DIFFRACTIONf_dihedral_angle_d14.788827
X-RAY DIFFRACTIONf_chiral_restr0.085341
X-RAY DIFFRACTIONf_plane_restr0.007398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.56-1.61580.19442260.1703368495
1.6158-1.68040.18782220.16263896100
1.6804-1.75690.17321880.15273923100
1.7569-1.84950.18772050.14283963100
1.8495-1.96530.18282010.14253914100
1.9653-2.1170.16682130.13543927100
2.117-2.32990.15851880.13543944100
2.3299-2.66670.1741960.13573958100
2.6667-3.35860.16282060.14633946100
3.3586-25.39740.15182120.1581389298
Refinement TLS params.Method: refined / Origin x: 23.9381 Å / Origin y: 9.3093 Å / Origin z: 6.7714 Å
111213212223313233
T0.0902 Å20.0024 Å20.0106 Å2-0.0859 Å20.0015 Å2--0.0982 Å2
L1.3048 °20.0309 °2-0.5208 °2-0.398 °2-0.237 °2--0.8421 °2
S0.0787 Å °0.0211 Å °0.1229 Å °0.0211 Å °-0.0121 Å °-0.0056 Å °-0.0845 Å °-0.0319 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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