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- PDB-2a3k: Crystal Structure of the Human Protein Tyrosine Phosphatase, PTPN... -

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Basic information

Entry
Database: PDB / ID: 2a3k
TitleCrystal Structure of the Human Protein Tyrosine Phosphatase, PTPN7 (HePTP, Hematopoietic Protein Tyrosine Phosphatase)
Componentsprotein tyrosine phosphatase, non-receptor type 7, isoform 1
KeywordsSIGNALING PROTEIN / PTPN7 / PHOSPHATASE / HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitotic spindle / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade ...Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitotic spindle / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade / 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
PHOSPHATE ION / : / Tyrosine-protein phosphatase non-receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBarr, A. / Turnbull, A.P. / Das, S. / Eswaran, J. / Debreczeni, J.E. / Longmann, E. / Smee, C. / Burgess, N. / Gileadi, O. / Sundstrom, M. ...Barr, A. / Turnbull, A.P. / Das, S. / Eswaran, J. / Debreczeni, J.E. / Longmann, E. / Smee, C. / Burgess, N. / Gileadi, O. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2006
Title: The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1.
Authors: Eswaran, J. / Debreczeni, J.E. / Longman, E. / Barr, A.J. / Knapp, S.
History
DepositionJun 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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: protein tyrosine phosphatase, non-receptor type 7, isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1575
Polymers33,7771
Non-polymers3804
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.125, 80.968, 100.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein protein tyrosine phosphatase, non-receptor type 7, isoform 1


Mass: 33777.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PNIC SGC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 18375658, UniProt: P35236*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.4 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 2.0M ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9207 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9207 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 10833 / Num. obs: 10833 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.48 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JLN

1jln


Resolution: 2.55→42.68 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / SU B: 23.061 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.66 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27466 522 4.8 %RANDOM
Rwork0.21897 ---
all0.22184 10366 --
obs0.22184 10366 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.008 Å2
Baniso -1Baniso -2Baniso -3
1--4.02 Å20 Å20 Å2
2--0.15 Å20 Å2
3---3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 20 32 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222205
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9653008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51923.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27615343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0211515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021691
X-RAY DIFFRACTIONr_nbd_refined0.210.2954
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.29
X-RAY DIFFRACTIONr_mcbond_it0.4571.51395
X-RAY DIFFRACTIONr_mcangle_it0.81722202
X-RAY DIFFRACTIONr_scbond_it1.2073923
X-RAY DIFFRACTIONr_scangle_it1.9134.5806
LS refinement shellResolution: 2.55→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 42 -
Rwork0.261 698 -
obs--93.08 %
Refinement TLS params.Method: refined / Origin x: 0.5937 Å / Origin y: -20.2486 Å / Origin z: -20.5802 Å
111213212223313233
T-0.0627 Å20.0142 Å2-0.012 Å2--0.0602 Å2-0.0121 Å2---0.033 Å2
L0.9888 °20.2251 °2-0.4369 °2-1.1878 °2-1.0577 °2--2.5728 °2
S-0.0333 Å °0.1676 Å °0.0885 Å °-0.2605 Å °0.0314 Å °0.0195 Å °0.1906 Å °0.0944 Å °0.0019 Å °

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