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- PDB-8xqd: The Crystal Structure of PTPRG from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xqd
TitleThe Crystal Structure of PTPRG from Biortus.
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsHYDROLASE / Possesses tyrosine phosphatase activity.
Function / homology
Function and homology information


negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of neuron projection development / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 / Fibronectin type III domain / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PTPRG from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionJan 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase gamma
B: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)72,1782
Polymers72,1782
Non-polymers00
Water3,963220
1
A: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)36,0891
Polymers36,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)36,0891
Polymers36,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.916, 76.161, 106.623
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 Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 36088.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG, PTPG / Production host: prokaryote coculture (bacteria) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.25 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaSCN, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18064 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18064 Å / Relative weight: 1
ReflectionResolution: 2.55→47.27 Å / Num. obs: 20006 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.3
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.675 / Num. unique obs: 2394

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.562 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27749 988 4.9 %RANDOM
Rwork0.21522 ---
obs0.2183 18972 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.619 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å2-0 Å20 Å2
2---1.1 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.55→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 0 220 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124725
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164439
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.6626398
X-RAY DIFFRACTIONr_angle_other_deg0.3441.57910189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.003534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68110826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2093.4782254
X-RAY DIFFRACTIONr_mcbond_other1.2093.4782253
X-RAY DIFFRACTIONr_mcangle_it2.1176.2282807
X-RAY DIFFRACTIONr_mcangle_other2.1176.2282808
X-RAY DIFFRACTIONr_scbond_it1.3023.6322471
X-RAY DIFFRACTIONr_scbond_other1.3013.6332472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2856.5973592
X-RAY DIFFRACTIONr_long_range_B_refined5.23542.1421055
X-RAY DIFFRACTIONr_long_range_B_other5.21842.220959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 80 -
Rwork0.312 1368 -
obs--100 %

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