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- PDB-2pbn: Crystal structure of the human tyrosine receptor phosphate gamma -

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Basic information

Entry
Database: PDB / ID: 2pbn
TitleCrystal structure of the human tyrosine receptor phosphate gamma
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / negative regulation of epithelial cell migration / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / negative regulation of neuron projection development / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 profile. / Tyrosine-specific protein phosphatases domain / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Reyes, C. / Pelletier, L. / Jin, X. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. ...Bonanno, J.B. / Freeman, J. / Bain, K.T. / Reyes, C. / Pelletier, L. / Jin, X. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT A MONOMER IS PROBABLY THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1852
Polymers36,0891
Non-polymers961
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.338, 107.338, 67.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsprobable monomer

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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.: 1 / Fragment: Tyrosine-protein phosphatase 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Sodium MES pH 6.5, 22% PEG 8000, 200mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→53.683 Å / Num. all: 49677 / Num. obs: 49677 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 16.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7108 / Rsym value: 0.645 / % possible all: 99

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Phasing

Phasing MRRfactor: 0.403 / Cor.coef. Fo:Fc: 0.629 / Cor.coef. Io to Ic: 0.586
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HY3

2hy3


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.158 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2485 5 %RANDOM
Rwork0.208 ---
obs0.209 49610 99.83 %-
all-49610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 5 238 2573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222389
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9353238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26723.802121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7411517
X-RAY DIFFRACTIONr_chiral_restr0.1150.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021820
X-RAY DIFFRACTIONr_nbd_refined0.2020.21120
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.214
X-RAY DIFFRACTIONr_mcbond_it1.2831.51468
X-RAY DIFFRACTIONr_mcangle_it1.94822317
X-RAY DIFFRACTIONr_scbond_it3.07531061
X-RAY DIFFRACTIONr_scangle_it4.8654.5920
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 160 -
Rwork0.409 3362 -
obs-3522 97.67 %

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