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- PDB-5e5u: Crystal structure of the complex between Carbonic anhydrase-like ... -

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Basic information

Entry
Database: PDB / ID: 5e5u
TitleCrystal structure of the complex between Carbonic anhydrase-like domain of PTPRG and Immunoglobulin domains 2-3 of CNTN6
Components
  • Contactin-6
  • Receptor-type tyrosine-protein phosphatase gamma
KeywordsCell Adhesion/Hydrolase / Neural cell adhesion molecule / Receptor-type protein tyrosine phosphatase / Immunoglobulin domains / Carbonic anhydrase-like domain / Cell Adhesion-Hydrolase complex
Function / homology
Function and homology information


dendrite self-avoidance / cell-cell adhesion mediator activity / negative regulation of epithelial cell migration / parallel fiber to Purkinje cell synapse / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / dephosphorylation / Notch signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...dendrite self-avoidance / cell-cell adhesion mediator activity / negative regulation of epithelial cell migration / parallel fiber to Purkinje cell synapse / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / dephosphorylation / Notch signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / axon guidance / negative regulation of neuron projection development / presynapse / presynaptic membrane / axon / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set 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 ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ACETIC ACID / FORMIC ACID / MALONATE ION / D-MALATE / Receptor-type tyrosine-protein phosphatase gamma / Contactin-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Contactin-6
C: Receptor-type tyrosine-protein phosphatase gamma
D: Contactin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,38318
Polymers104,6814
Non-polymers1,70214
Water9,638535
1
A: Receptor-type tyrosine-protein phosphatase gamma
B: Contactin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,17710
Polymers52,3412
Non-polymers8378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint1 kcal/mol
Surface area21460 Å2
MethodPISA
2
C: Receptor-type tyrosine-protein phosphatase gamma
D: Contactin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2058
Polymers52,3412
Non-polymers8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint3 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.641, 113.530, 117.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 30006.334 Da / Num. of mol.: 2 / Fragment: CA domain, UNP residues 57-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprg / Plasmid: pET32HP / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: Q05909, protein-tyrosine-phosphatase
#2: Protein Contactin-6 / / Neural recognition molecule NB-3 / mNB-3


Mass: 22334.201 Da / Num. of mol.: 2 / Fragment: Immunoglobulin domains 2-3, UNP residues 119-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn6 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Shuffle Express / References: UniProt: Q9JMB8

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Non-polymers , 6 types, 549 molecules

#3: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 55% (v/v) Tacsimate pH 7.0, 150 mM NDSB 201

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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: Mar 13, 2013
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→50 Å / Num. obs: 70482 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.65 Å2 / Rmerge(I) obs: 0.096 / Χ2: 0.958 / Net I/av σ(I): 19.509 / Net I/σ(I): 6.4 / Num. measured all: 500144
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.075.30.59362880.90989.2
2.07-2.156.30.50969340.90598.2
2.15-2.2570.40870141.03299.8
2.25-2.377.50.32370690.906100
2.37-2.527.50.24771030.894100
2.52-2.717.50.18471070.912100
2.71-2.997.50.12470950.982100
2.99-3.427.50.08871770.997100
3.42-4.317.50.08672110.94699.9
4.31-507.20.04474841.06899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å40.75 Å
Translation2.5 Å40.75 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Coot0.8.1model building
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KLD

3kld


Resolution: 2→24.891 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 3517 5 %
Rwork0.1676 66840 -
obs0.17 70357 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.16 Å2 / Biso mean: 40.7988 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 2→24.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 112 535 8039
Biso mean--71.98 41.55 -
Num. residues----926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077710
X-RAY DIFFRACTIONf_angle_d1.04910442
X-RAY DIFFRACTIONf_chiral_restr0.0441078
X-RAY DIFFRACTIONf_plane_restr0.0051378
X-RAY DIFFRACTIONf_dihedral_angle_d13.382822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.02770.27881120.22522251236383
2.0277-2.05670.29551370.21982423256090
2.0567-2.08740.28191140.21392549266396
2.0874-2.120.27771480.20372592274097
2.12-2.15470.2491440.20742679282399
2.1547-2.19180.27291390.193926562795100
2.1918-2.23170.27771330.199326952828100
2.2317-2.27460.26141500.192226582808100
2.2746-2.3210.24041350.185826952830100
2.321-2.37140.22991410.192126762817100
2.3714-2.42650.22091410.187927112852100
2.4265-2.48710.25971520.195426602812100
2.4871-2.55430.27021340.202927112845100
2.5543-2.62940.26321380.200926992837100
2.6294-2.71420.28051450.203126962841100
2.7142-2.81110.29111450.20927072852100
2.8111-2.92340.26291470.205327052852100
2.9234-3.05630.22881380.188426892827100
3.0563-3.21710.2541450.187827242869100
3.2171-3.41820.21831400.16727412881100
3.4182-3.68130.1921470.150427172864100
3.6813-4.05040.16511440.138727622906100
4.0504-4.63320.16581460.119827472893100
4.6332-5.8250.17011470.126327912938100
5.825-24.89270.17591550.148729063061100
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)
12.3235-0.3607-0.80511.5482-0.58563.02510.0158-0.09170.39140.12420.14290.0321-0.2797-0.1246-0.14660.19330.0251-0.02720.2432-0.0130.300755.001764.827363.8056
25.4839-0.6822.04224.4007-1.03615.5361-0.059-0.129-0.31050.1089-0.017-0.02290.17490.05460.02880.21810.02140.03820.174-0.01540.174680.89236.099254.3414
37.55012.58431.02981.74130.80161.9297-0.06690.02840.1053-0.2160.00710.0185-0.22590.24010.04230.25720.01260.0160.28050.06410.163689.631757.013748.8632
42.64680.61280.20171.38480.21192.17220.0127-0.01060.2186-0.0045-0.0119-0.0042-0.15220.11260.00740.1726-0.0172-0.02180.1690.00340.18486.677455.460183.5103
53.98-0.53912.01343.9715-0.36474.5863-0.17120.41430.1468-0.30320.10940.0874-0.05960.05530.00780.2753-0.1179-0.01860.1951-0.03250.236558.341531.730270.7996
65.2639-2.5645-0.53313.5683-0.23191.8274-0.0514-0.0994-0.16220.12120.00140.38840.0494-0.45460.00780.1974-0.0533-0.01260.2973-0.04240.200551.862942.120890.2212
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 118:221))B0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 222:316))B0
4X-RAY DIFFRACTION4chain 'C' and ((resseq 56:320))C56 - 320
5X-RAY DIFFRACTION5chain 'D' and ((resseq 118:221))D0
6X-RAY DIFFRACTION6chain 'D' and ((resseq 222:316))D0

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