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- PDB-5e5r: Crystal structure of the complex between Carbonic anhydrase-like ... -

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Basic information

Entry
Database: PDB / ID: 5e5r
TitleCrystal structure of the complex between Carbonic anhydrase-like domain of PTPRG and Immunoglobulin domains 2-3 of CNTN3
Components
  • Contactin-3
  • Receptor-type tyrosine-protein phosphatase gamma
KeywordsHydrolase/Cell Adhesion / Neural cell adhesion molecule / Receptor-type protein tyrosine phosphatase / Immunoglobulin domains / Carbonic anhydrase-like domain / Hydrolase-Cell Adhesion complex
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / side of membrane / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway ...Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / side of membrane / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / negative regulation of neuron projection development / cell adhesion / signal transduction / extracellular exosome / 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 / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Carbonic Anhydrase II ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / 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
FORMIC ACID / MALONATE ION / Receptor-type tyrosine-protein phosphatase gamma / Contactin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsNikolaienko, R.M. / Bouyain, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088806 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.
Authors: Nikolaienko, R.M. / Hammel, M. / Dubreuil, V. / Zalmai, R. / Hall, D.R. / Mehzabeen, N. / Karuppan, S.J. / Harroch, S. / Stella, S.L. / Bouyain, S.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 gamma
B: Contactin-3
C: Receptor-type tyrosine-protein phosphatase gamma
D: Contactin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2289
Polymers103,8304
Non-polymers3985
Water1,06359
1
A: Receptor-type tyrosine-protein phosphatase gamma
B: Contactin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0173
Polymers51,9152
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Receptor-type tyrosine-protein phosphatase gamma
D: Contactin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2116
Polymers51,9152
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.138, 90.526, 147.448
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 Receptor-type tyrosine-protein phosphatase gamma / R-PTP-gamma


Mass: 30272.697 Da / Num. of mol.: 2 / Fragment: CA domain, UNP residues 56-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG, PTPG / Plasmid: pET32HP / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Protein Contactin-3 / Brain-derived immunoglobulin superfamily protein 1 / BIG-1 / Plasmacytoma-associated neuronal glycoprotein


Mass: 21642.453 Da / Num. of mol.: 2 / Fragment: Immunoglobulin domains 2-3, UNP residues 124-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn3, Pang, Pcs / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Shuffle Express / References: UniProt: Q07409
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1% (v/v) Tacsimate pH 7.0, 20% (w/v) PEG 3350, 50mM Imidazole-HCl pH 6.5

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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: May 1, 2011
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31166 / % possible obs: 99.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 56.08 Å2 / Rmerge(I) obs: 0.134 / Χ2: 1.02 / Net I/av σ(I): 7.237 / Net I/σ(I): 8.3 / Num. measured all: 356562
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.695.30.58829531.07396.3
2.69-2.880.47630660.97399.8
2.8-2.9310.20.39330961.015100
2.93-3.0811.30.28530860.941100
3.08-3.28120.22530730.951100
3.28-3.5312.60.18831270.979100
3.53-3.8813.20.14731111.024100
3.88-4.4513.90.12131411.112100
4.45-5.6140.11331761.079100
5.6-5013.30.10333371.03199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å49.15 Å
Translation2.6 Å49.15 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JXH, 5E4I

3jxh

5e4i


Resolution: 2.6→49.149 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1553 5 %
Rwork0.1873 29486 -
obs0.1904 31039 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.64 Å2 / Biso mean: 71.2232 Å2 / Biso min: 24.46 Å2
Refinement stepCycle: final / Resolution: 2.6→49.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7205 0 27 59 7291
Biso mean--98.31 49.93 -
Num. residues----901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097425
X-RAY DIFFRACTIONf_angle_d1.10110054
X-RAY DIFFRACTIONf_chiral_restr0.0431054
X-RAY DIFFRACTIONf_plane_restr0.0051325
X-RAY DIFFRACTIONf_dihedral_angle_d14.0132730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.68380.33911330.26662529266295
2.6838-2.77970.37381390.24772633277299
2.7797-2.8910.33941400.25226562796100
2.891-3.02250.30491410.243226552796100
3.0225-3.18190.31521390.237526622801100
3.1819-3.38120.331420.2326862828100
3.3812-3.64220.26561400.203726732813100
3.6422-4.00850.28211420.19322688283099
4.0085-4.58820.23291410.15292702284399
4.5882-5.77920.16831440.144527312875100
5.7792-49.15810.19681520.15872871302399
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)
14.62851.65270.77528.6906-1.35285.7250.5948-1.00180.54691.2093-0.69450.4008-0.7238-0.09950.10150.5856-0.10630.12270.6535-0.14150.3219-50.8968-30.162726.6603
27.0585-1.8588-2.0728.4455-0.46398.5221-0.655-0.3695-1.30760.56270.08130.36031.6062-0.0560.55970.7823-0.11770.12960.45160.05550.4836-59.1349-62.07758.0005
37.61050.1366-4.6612.8321.72288.9292-0.59291.14330.2597-0.69840.20890.1894-0.1797-0.61120.41570.6385-0.2102-0.18060.49540.05950.3857-53.3906-46.0216-7.1526
45.5282.3702-1.99416.1894-0.4224.9602-0.44340.946-0.0926-0.79020.4963-0.61320.03810.0242-0.06180.3818-0.10120.04770.4762-0.04660.2915-15.1068-20.731645.2127
58.12940.50343.50436.9970.6648.2253-0.2538-0.14990.55140.4235-0.0788-0.1909-1.09360.05140.32930.5033-0.00970.09580.2381-0.04470.329-25.9765-7.500179.5404
64.8729-4.92125.59127.5844-7.10768.72540.0259-0.1330.05-0.042-0.0639-0.24410.2498-0.00850.06250.4422-0.08450.16380.2954-0.11550.3969-21.6258-29.891981.098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 56:320))A56 - 320
2X-RAY DIFFRACTION2chain 'B' and ((resseq 125:221))B0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 222:316))B0
4X-RAY DIFFRACTION4chain 'C' and ((resseq 57:320))C57 - 320
5X-RAY DIFFRACTION5chain 'D' and ((resseq 124:221))D0
6X-RAY DIFFRACTION6chain 'D' and ((resseq 222:316))D0

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