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- PDB-2cjz: crystal structure of the c472s mutant of human protein tyrosine p... -

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Basic information

Entry
Database: PDB / ID: 2cjz
Titlecrystal structure of the c472s mutant of human protein tyrosine phosphatase ptpn5 (step, striatum enriched phosphatase) in complex with phosphotyrosine
ComponentsHUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / STEP / PTPN5 / PHOSPHATASE
Function / homology
Function and homology information


Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue 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 / cell junction / endoplasmic reticulum membrane ...Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue 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 / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / 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 ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / 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
O-PHOSPHOTYROSINE / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDebreczeni, J.E. / Barr, A.J. / Eswaran, J. / Smee, C. / Burgess, N. / Gileadi, O. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Debreczeni, J.E. / Barr, A.J. / Eswaran, J. / Smee, C. / Burgess, N. / Gileadi, O. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Knapp, S. / von Delft, F.
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.F. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionApr 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.6Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5123
Polymers35,1891
Non-polymers3232
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.342, 64.348, 100.781
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 HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 / PROTEIN-TYROSINE PHOSPHATASE STRIATUM-ENRICHED / STEP / NEURAL- SPECIFIC PROTEIN-TYROSINE PHOSPHATASE


Mass: 35188.777 Da / Num. of mol.: 1 / Fragment: PHOSPHATASE DOMAIN, RESIDUES 258-539 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54829, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 472 TO SER
Sequence detailsRESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE UNIPROT ENTRY P54829 ...RESIDUES ASP 289, LEU 298, VAL 299 AND THR 517 ARE GIVEN AS VARIANTS IN THE UNIPROT ENTRY P54829 AND REFERNCED IN PUBMED ID: 14702039. RESIDUES -23 TO -1 FORM PART OF A N-TERMINAL HIS-TAG USED FOR EXPRESSION

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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: 48 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 150 NL SITTING DROPS, 0.1 M CACL2, 0.1 M TRIS PH 8, 20% PEG 6K, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.7→50.39 Å / Num. obs: 37692 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.92
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.31 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.07 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIJ

2bij


Resolution: 1.7→101.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.529 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1888 5 %RANDOM
Rwork0.175 ---
obs0.177 35803 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→101.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 20 212 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222286
X-RAY DIFFRACTIONr_bond_other_d0.0010.021540
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9523116
X-RAY DIFFRACTIONr_angle_other_deg0.82533754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2735280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76923.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8491514
X-RAY DIFFRACTIONr_chiral_restr0.0660.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
X-RAY DIFFRACTIONr_nbd_refined0.2070.2426
X-RAY DIFFRACTIONr_nbd_other0.1880.21561
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21100
X-RAY DIFFRACTIONr_nbtor_other0.0810.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.75451437
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.65372269
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6679983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3211843
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 133
Rwork0.23 2241
Refinement TLS params.Method: refined / Origin x: 15.205 Å / Origin y: -5.427 Å / Origin z: -16.077 Å
111213212223313233
T-0.0253 Å2-0.0043 Å20.0017 Å2--0.0525 Å20.0139 Å2---0.0409 Å2
L0.2967 °2-0.0679 °2-0.3212 °2-0.6802 °20.0389 °2--1.2861 °2
S-0.0045 Å °0.0025 Å °-0.0112 Å °0.0123 Å °0.0196 Å °0.1004 Å °0.0268 Å °-0.1081 Å °-0.0152 Å °

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