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- PDB-2qdp: Crystal structure of the HePTP catalytic domain C270S mutant crys... -

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Basic information

Entry
Database: PDB / ID: 2qdp
TitleCrystal structure of the HePTP catalytic domain C270S mutant crystallized in ammonium acetate
ComponentsTyrosine-protein phosphatase non-receptor type 7
KeywordsHYDROLASE / HePTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7
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 / cytoplasmic side of plasma membrane / mitotic spindle / 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 / cytoplasmic side of plasma membrane / mitotic spindle / 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: 2.72 Å
AuthorsCritton, D.A. / Tortajada, A. / Page, R.
CitationJournal: To be published
Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.
Authors: Critton, D.A. / Tortajada, A. / Stetson, G. / Peti, W. / Page, R.
History
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4152
Polymers35,3201
Non-polymers951
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.131, 127.131, 60.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 35319.926 Da / Num. of mol.: 1 / Fragment: Catalytic domain (residues 65-360) / Mutation: C270S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.07 M AMMONIUM ACETATE, 0.07 M BIS-TRIS, 12% POLYETHYLENE GLYCOL 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 2006
Details: Si(111) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR
RadiationMonochromator: Si(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. all: 15103 / Num. obs: 14980 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.6
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.601 / % possible all: 98.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å34.29 Å
Translation2.72 Å34.29 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZC0

1zc0


Resolution: 2.72→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.093 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22681 752 5 %RANDOM
Rwork0.15709 ---
obs0.16055 14314 99.33 %-
all-14410 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.72→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 5 132 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg21.963246
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0555291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23123.628113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0461519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021841
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.21605
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.86231501
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.55552373
X-RAY DIFFRACTIONr_scbond_it7.581005
X-RAY DIFFRACTIONr_scangle_it10.12811873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.719→2.789 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 53 -
Rwork0.252 1026 -
obs--97.91 %
Refinement TLS params.Method: refined / Origin x: 43.8 Å / Origin y: 44.3944 Å / Origin z: 9.9146 Å
111213212223313233
T-0.0824 Å20.0524 Å20.0657 Å2--0.0632 Å20.0347 Å2---0.076 Å2
L2.2861 °2-0.5655 °20.8784 °2-1.8606 °20.0385 °2--1.0709 °2
S0.1512 Å °0.0869 Å °-0.0199 Å °-0.0575 Å °-0.0366 Å °-0.0654 Å °-0.0657 Å °-0.1271 Å °-0.1146 Å °

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