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- PDB-2i75: Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4) -

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Basic information

Entry
Database: PDB / ID: 2i75
TitleCrystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4)
ComponentsTyrosine-protein phosphatase non-receptor type 4
KeywordsHYDROLASE / PTPN4 / PTP / tyrosine phosphatase / MEG-1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / glutamate receptor binding / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / glutamate receptor binding / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / 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 / cytoskeleton / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain ...Protein-tyrosine phosphatase, non-receptor type-3, -4 / PTPN3/4, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / Protein tyrosine phosphatase superfamily / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsUgochukwu, E. / Barr, A. / Savitsky, P. / Burgess, N. / Das, S. / Turnbull, A. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. ...Ugochukwu, E. / Barr, A. / Savitsky, P. / Burgess, N. / Das, S. / Turnbull, A. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / 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
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8743
Polymers36,6821
Non-polymers1922
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.075, 66.075, 144.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 4 / Protein-tyrosine phosphatase MEG1 / PTPase-MEG1 / MEG


Mass: 36681.641 Da / Num. of mol.: 1 / Fragment: PTPN4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)R3 / References: UniProt: P29074, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M HEPES, 0.1 M NaCl, 1.3 M (NH4)SO4. , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→38.92 Å / Num. all: 11901 / Num. obs: 11901 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.45→2.58 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B49

2b49


Resolution: 2.45→38.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 22.541 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29104 582 4.9 %RANDOM
Rwork0.22359 ---
obs0.22671 11249 95.38 %-
all-11249 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.129 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2--2.22 Å20 Å2
3----4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 10 51 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222144
X-RAY DIFFRACTIONr_bond_other_d0.0010.021396
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9522918
X-RAY DIFFRACTIONr_angle_other_deg1.08933413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60124.20588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.131510
X-RAY DIFFRACTIONr_chiral_restr0.1310.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_nbd_refined0.2110.2415
X-RAY DIFFRACTIONr_nbd_other0.1960.21392
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21048
X-RAY DIFFRACTIONr_nbtor_other0.0870.21086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.21
X-RAY DIFFRACTIONr_mcbond_it0.4591.51394
X-RAY DIFFRACTIONr_mcbond_other0.0861.5545
X-RAY DIFFRACTIONr_mcangle_it0.72422197
X-RAY DIFFRACTIONr_scbond_it1.1113865
X-RAY DIFFRACTIONr_scangle_it1.6934.5721
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 41 -
Rwork0.283 818 -
obs--97.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
113.1629-4.1668-1.766.263-3.03417.6933-1.2425-0.161-0.4689-1.11010.2507-0.74441.56830.38860.99170.83820.34140.2777-0.0058-0.00440.0165-1.338117.6247-25.517
21.12840.338-0.17823.0638-2.95079.02590.0248-0.10320.00130.15510.0573-0.0266-0.5258-0.5544-0.0821-0.17390.08710.013-0.114-0.0004-0.1107-12.344532.04760.7959
35.3616-2.2151-2.33773.9563-0.15069.542-0.0613-0.4639-0.2348-0.29750.00160.08321.1157-0.2270.05970.0849-0.1501-0.0712-0.0390.0791-0.0595-11.878517.51696.4163
41.9905-0.3194-1.17833.2438-1.66729.1434-0.12580.1586-0.3648-0.76590.0255-0.00251.2884-0.17890.10030.12130.024-0.0101-0.16830.0036-0.0635-9.436821.6981-10.8162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA638 - 65330 - 45
2X-RAY DIFFRACTION2AA654 - 70146 - 93
3X-RAY DIFFRACTION2AA703 - 71695 - 108
4X-RAY DIFFRACTION2AA719 - 778111 - 170
5X-RAY DIFFRACTION3AA779 - 831171 - 223
6X-RAY DIFFRACTION4AA832 - 913224 - 305

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