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- PDB-3jxg: CA-like domain of mouse PTPRG -

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Basic information

Entry
Database: PDB / ID: 3jxg
TitleCA-like domain of mouse PTPRG
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsCELL ADHESION / CA-like domain / Glycoprotein / Hydrolase / Membrane / Phosphoprotein / Protein phosphatase / Transmembrane
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of neuron projection development / extracellular space / identical protein binding / 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 / Carbonic Anhydrase II / Alpha carbonic anhydrase / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...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 / Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBouyain, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules.
Authors: Bouyain, S. / Watkins, D.J.
History
DepositionSep 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Receptor-type tyrosine-protein phosphatase gamma
D: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)121,4474
Polymers121,4474
Non-polymers00
Water12,412689
1
A: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)30,3621
Polymers30,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)30,3621
Polymers30,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)30,3621
Polymers30,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Receptor-type tyrosine-protein phosphatase gamma


Theoretical massNumber of molelcules
Total (without water)30,3621
Polymers30,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.756, 85.140, 91.065
Angle α, β, γ (deg.)90.000, 115.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 30361.684 Da / Num. of mol.: 4
Fragment: carbonic anhydrase-like domain (UNP residues 55-320)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprg / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI2(DE3) / References: UniProt: Q05909, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Na-HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2009
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 123224 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.088 / Χ2: 1.047 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.762.80.51109771.09688.4
1.76-1.833.20.448122041.0798.2
1.83-1.913.70.347124611.08100
1.91-2.023.70.249124651.114100
2.02-2.143.70.18124321.051100
2.14-2.313.70.134125031.028100
2.31-2.543.80.099124611.017100
2.54-2.913.80.073125190.977100
2.91-3.663.80.058125461.074100
3.66-503.70.078126560.99499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.28
Highest resolutionLowest resolution
Rotation2.5 Å36.8 Å
Translation2.5 Å36.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.801 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.864 / SU ML: 0.22 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 5694 4.87 %
Rwork0.173 --
obs0.175 117021 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.044 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 124.14 Å2 / Biso mean: 32.702 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.164 Å2-0 Å21.598 Å2
2---6.407 Å2-0 Å2
3---6.571 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8347 0 0 689 9036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098604
X-RAY DIFFRACTIONf_angle_d1.20611676
X-RAY DIFFRACTIONf_chiral_restr0.091205
X-RAY DIFFRACTIONf_plane_restr0.0061530
X-RAY DIFFRACTIONf_dihedral_angle_d17.4083030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.3031180.2512595271365
1.72-1.740.2661510.2312992314376
1.74-1.7610.2661600.2273154331480
1.761-1.7830.2791580.2193247340582
1.783-1.8070.2431760.2083443361987
1.807-1.8320.2541650.2043410357587
1.832-1.8580.2551830.1943611379490
1.858-1.8850.2091920.1983516370890
1.885-1.9150.261920.1833638383092
1.915-1.9460.2351860.1793687387394
1.946-1.980.2281950.1713781397694
1.98-2.0160.2251900.1693723391395
2.016-2.0550.1991950.1663805400096
2.055-2.0960.1952030.163796399997
2.096-2.1420.1891950.163852404797
2.142-2.1920.1971970.1623870406798
2.192-2.2470.2022030.1673866406997
2.247-2.3070.2281910.1653891408298
2.307-2.3750.1922080.1663878408698
2.375-2.4520.2161960.1733893408999
2.452-2.540.2082010.1773903410499
2.54-2.6410.222080.1743937414599
2.641-2.7610.2262040.1813969417399
2.761-2.9070.2341970.18139234120100
2.907-3.0890.2232060.18539664172100
3.089-3.3270.1912040.17739794183100
3.327-3.6620.1742030.15939734176100
3.662-4.1910.1622020.14639964198100
4.191-5.2780.1472080.13340064214100
5.278-36.8090.2052070.184027423499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13060.0522-0.06691.75850.32591.13350.0062-0.02650.03220.0149-0.02740.2327-0.0117-0.04750.02120.0911-0.00650.01890.14940.00180.1611-16.073864.299834.8677
21.063-0.35450.20261.7614-0.13990.69890.0018-0.0278-0.02140.033-0.0238-0.0350.00520.01220.01910.09420.00120.010.13180.00230.088724.117943.593837.7231
30.88540.4471-0.04041.91940.60040.86110.01320.011-0.0467-0.0895-0.04410.0338-0.0164-0.04220.02880.14610.0119-0.02290.12320.00390.09162.205146.66542.8881
42.2309-1.6151-1.1363.56561.32151.8075-0.07150.066-0.16150.1367-0.01010.35950.0959-0.08790.0930.19030.02580.03340.1862-0.01970.155939.376324.99554.3522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA58 - 320
2X-RAY DIFFRACTION2chain BB58 - 320
3X-RAY DIFFRACTION3chain CC57 - 320
4X-RAY DIFFRACTION4chain DD58 - 320

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