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- PDB-3kld: PTPRG CNTN4 complex -

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Basic information

Entry
Database: PDB / ID: 3kld
TitlePTPRG CNTN4 complex
Components
  • Contactin 4
  • Receptor-type tyrosine-protein phosphatase gamma
KeywordsCELL ADHESION / PROTEIN COMPLEX / RECEPTOR PROTEIN TYROSINE PHOSPHATASE / NEURAL RECOGNITION MOLECULE / Glycoprotein / Membrane / Phosphoprotein / Protein phosphatase / Transmembrane
Function / homology
Function and homology information


negative regulation of neuron differentiation / side of membrane / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein dephosphorylation / brain development / neuron projection development / nervous system development / cell adhesion / extracellular region ...negative regulation of neuron differentiation / side of membrane / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein dephosphorylation / brain development / neuron projection development / nervous system development / cell adhesion / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Immunoglobulin I-set / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set domain ...: / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Immunoglobulin I-set / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase gamma / Contactin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 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
DepositionNov 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin 4
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1666
Polymers73,2812
Non-polymers8854
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.432, 138.957, 50.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Contactin 4 / AxCAM / BIG-2


Mass: 42919.570 Da / Num. of mol.: 1 / Fragment: Ig domains 1-4 (UNP residues 25-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CNTN4 / Plasmid: pSGHP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q14BL8
#2: Protein Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 30361.684 Da / Num. of mol.: 1
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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 1500 - 50 mM Sodium cacodylate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 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→40 Å / Num. obs: 46797 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.156 / Χ2: 1.027 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3857 / Χ2: 0.931 / % possible all: 80.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.64
Highest resolutionLowest resolution
Rotation2.5 Å37.87 Å
Translation2.5 Å37.87 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: 1.999→37.867 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2254 5.02 %RANDOM
Rwork0.179 ---
obs0.182 44869 91.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.871 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 181.5 Å2 / Biso mean: 36.5 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-13.783 Å2-0 Å2-0 Å2
2---7.85 Å20 Å2
3----5.933 Å2
Refinement stepCycle: LAST / Resolution: 1.999→37.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 56 415 5538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115263
X-RAY DIFFRACTIONf_angle_d1.3547141
X-RAY DIFFRACTIONf_chiral_restr0.093771
X-RAY DIFFRACTIONf_plane_restr0.006930
X-RAY DIFFRACTIONf_dihedral_angle_d17.1521918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.999-2.0420.3121150.221984209970
2.042-2.090.3231130.2022179229276
2.09-2.1420.241200.1932335245581
2.142-2.20.2861270.1822396252384
2.2-2.2650.231280.1922461258987
2.265-2.3380.2721390.1882614275391
2.338-2.4210.2781420.1852724286694
2.421-2.5180.2361480.1852762291096
2.518-2.6330.2671440.1822747289196
2.633-2.7720.2671480.1942796294497
2.772-2.9450.2611500.1922833298398
2.945-3.1720.2541520.1952886303899
3.172-3.4910.2231520.18628903042100
3.491-3.9960.2081550.16629323087100
3.996-5.0330.1781560.13929663122100
5.033-37.8730.1921650.16531103275100
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)
1-0.10030.7175-0.30490.5138-0.40650.87050.1114-0.00650.13050.1020.01360.5074-0.2853-0.0311-0.08860.30880.0457-0.02070.11350.02230.242411.959751.081121.5854
20.6367-0.052-0.4242.4752-0.57110.17030.0466-0.01490.0466-0.35020.13820.76520.06640.0071-0.17790.1877-0.0147-0.0410.16640.05750.391912.077275.2566-11.4419
30.5460.0416-0.28231.70640.01560.31450.0729-0.03010.0538-0.4668-0.0994-0.0076-0.04560.04290.00690.24540.03790.03030.1180.01380.128129.25260.7374-12.769
40.5271-0.04430.00780.6621-0.1092-0.0985-0.02190.01470.00890.10440.0384-0.06150.091-0.0495-0.0120.1909-0.02220.00020.1671-00.116732.928835.959222.269
50.74080.00550.04970.97150.12671.1705-0.037-0.0625-0.01280.15260.0156-0.0672-0.04790.25010.01620.1559-0.0030.00450.19320.00980.123340.848996.5695-3.6802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 25:121A25 - 121
2X-RAY DIFFRACTION2chain A and resid 122:224A122 - 224
3X-RAY DIFFRACTION3chain A and resid 225:314A225 - 314
4X-RAY DIFFRACTION4chain A and resid 315:402A315 - 402
5X-RAY DIFFRACTION5chain BB56 - 320

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