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- PDB-2oc3: Crystal Structure of the Catalytic Domain of Human Protein Tyrosi... -

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Basic information

Entry
Database: PDB / ID: 2oc3
TitleCrystal Structure of the Catalytic Domain of Human Protein Tyrosine Phosphatase non-receptor Type 18
ComponentsTyrosine-protein phosphatase non-receptor type 18
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / Receptor / Human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / blastocyst formation / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus ...negative regulation of ERBB signaling pathway / blastocyst formation / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus / cytoplasm / cytosol
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 ...: / : / 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
Tyrosine-protein phosphatase non-receptor type 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUgochukwu, E. / Barr, A. / Alfano, I. / Gorrec, F. / Umeano, C. / Savitsky, P. / Sobott, F. / Eswaran, J. / Papagrigoriou, E. / Debreczeni, J.E. ...Ugochukwu, E. / Barr, A. / Alfano, I. / Gorrec, F. / Umeano, C. / Savitsky, P. / Sobott, F. / Eswaran, J. / Papagrigoriou, E. / Debreczeni, J.E. / Turnbull, A. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 18


Theoretical massNumber of molelcules
Total (without water)34,2961
Polymers34,2961
Non-polymers00
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.338, 63.763, 48.992
Angle α, β, γ (deg.)90.00, 102.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 18 / Brain-derived phosphatase


Mass: 34296.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN18 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) phage resistant / References: UniProt: Q99952, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 0.1M HEPES, 25% PEG-3350, 6% Jeffamine M-600, pH 6.8, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97875
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 1.5→38.24 Å / Num. obs: 44277 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.4 / Num. unique all: 19366 / Rsym value: 0.343 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2B49, 1GWZ

2b49

1gwz


Resolution: 1.5→38.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.069 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18395 2228 5 %RANDOM
Rwork0.15407 ---
all0.15557 42028 --
obs0.15557 42028 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.822 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.24 Å2
2---0.3 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 0 277 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222285
X-RAY DIFFRACTIONr_bond_other_d0.0010.021570
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9563110
X-RAY DIFFRACTIONr_angle_other_deg0.9333819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92322.92999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7115392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2191519
X-RAY DIFFRACTIONr_chiral_restr0.090.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
X-RAY DIFFRACTIONr_nbd_refined0.2160.2416
X-RAY DIFFRACTIONr_nbd_other0.2040.21643
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21134
X-RAY DIFFRACTIONr_nbtor_other0.0850.21172
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_mcbond_it3.36451464
X-RAY DIFFRACTIONr_mcbond_other1.085570
X-RAY DIFFRACTIONr_mcangle_it4.05272291
X-RAY DIFFRACTIONr_scbond_it5.0719957
X-RAY DIFFRACTIONr_scangle_it6.54311810
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 156 -
Rwork0.209 2812 -
obs--90.63 %

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