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- PDB-3jxf: CA-like domain of human PTPRZ -

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Basic information

Entry
Database: PDB / ID: 3jxf
TitleCA-like domain of human PTPRZ
ComponentsReceptor-type tyrosine-protein phosphatase zeta
KeywordsCELL ADHESION / CA-like domain / Alternative splicing / Glycoprotein / Hydrolase / Membrane / Polymorphism / Protein phosphatase / Transmembrane
Function / homology
Function and homology information


perineuronal net / regulation of oligodendrocyte progenitor proliferation / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / regulation of myelination / Other interleukin signaling / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / positive regulation of oligodendrocyte differentiation / hematopoietic progenitor cell differentiation ...perineuronal net / regulation of oligodendrocyte progenitor proliferation / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / regulation of myelination / Other interleukin signaling / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / positive regulation of oligodendrocyte differentiation / hematopoietic progenitor cell differentiation / protein dephosphorylation / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine phosphatase activity / central nervous system development / neuron projection development / integrin binding / negative regulation of neuron apoptotic process / learning or memory / synapse / signal transduction / extracellular region / 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 / 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 zeta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.004 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,6592
Polymers61,6592
Non-polymers00
Water3,999222
1
A: Receptor-type tyrosine-protein phosphatase zeta


Theoretical massNumber of molelcules
Total (without water)30,8301
Polymers30,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase zeta


Theoretical massNumber of molelcules
Total (without water)30,8301
Polymers30,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.963, 68.118, 65.682
Angle α, β, γ (deg.)90.000, 98.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase zeta / R-PTP-zeta / R-PTP-zeta-2 / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein- ...R-PTP-zeta / R-PTP-zeta-2 / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine phosphatase receptor type Z polypeptide 2


Mass: 30829.646 Da / Num. of mol.: 2 / Fragment: N-terminal CA-like domain (UNP residues 34-302)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTPZP2, PTPRZ, PTPRZ1, PTPRZ2, PTPZ / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI2(DE3) / References: UniProt: P23471, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Na-cacodylate pH 6.5, 200 mM Magnesium acetate, 20% PEG 8000, 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / 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: 2→50 Å / Num. obs: 37363 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.115 / Χ2: 1.052 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.072.90.38136441.10999.3
2.07-2.153.30.33537141.05699.9
2.15-2.253.60.29837441.11299.9
2.25-2.373.70.25837101.122100
2.37-2.523.70.20137391.046100
2.52-2.713.80.16837391.061100
2.71-2.993.80.13937231.052100
2.99-3.423.80.11637471.009100
3.42-4.313.80.09337710.988100
4.31-503.70.07238320.99399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.81
Highest resolutionLowest resolution
Rotation2.5 Å35.94 Å
Translation2.5 Å35.94 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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→35.943 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.845 / SU ML: 0.25 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1930 5.36 %RANDOM
Rwork0.175 ---
obs0.177 36026 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.736 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 137.74 Å2 / Biso mean: 34.831 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--3.849 Å20 Å2-5.592 Å2
2---6.061 Å2-0 Å2
3---4.688 Å2
Refinement stepCycle: LAST / Resolution: 2.004→35.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 0 222 4533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064412
X-RAY DIFFRACTIONf_angle_d0.9695956
X-RAY DIFFRACTIONf_chiral_restr0.067644
X-RAY DIFFRACTIONf_plane_restr0.003765
X-RAY DIFFRACTIONf_dihedral_angle_d16.5951591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.004-2.0540.3081100.2132052216281
2.054-2.110.2341280.1962301242992
2.11-2.1720.231370.1812331246891
2.172-2.2420.2831300.1852373250395
2.242-2.3220.2541390.22411255095
2.322-2.4150.2641460.1882441258796
2.415-2.5250.2681390.192454259397
2.525-2.6580.2281410.1912473261498
2.658-2.8250.2471350.1962499263498
2.825-3.0430.2651420.1882506264899
3.043-3.3490.2021430.1762532267599
3.349-3.8320.1721440.1525532697100
3.832-4.8270.1651450.13825652710100
4.827-35.9480.1991510.16326052756100
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)
10.888-0.24260.22331.0477-0.18780.9138-0.0951-0.06310.07390.09230.05650.0832-0.0621-0.04220.03630.12150.00890.02080.1108-0.00620.14352.959728.960513.1386
20.96760.60270.34331.47820.30811.0256-0.05380.0170.0331-0.1369-0.02640.0951-0.0009-0.01870.07210.09610.0050.01620.112-0.00630.13233.431625.94-13.1774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA34 - 301
2X-RAY DIFFRACTION2chain BB31 - 301

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