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- PDB-3jxa: Immunoglobulin domains 1-4 of mouse CNTN4 -

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Basic information

Entry
Database: PDB / ID: 3jxa
TitleImmunoglobulin domains 1-4 of mouse CNTN4
ComponentsContactin 4
KeywordsCELL ADHESION / Immunoglobulin-like domains / Horseshoe-like conformation / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of neuron differentiation / side of membrane / brain development / neuron projection development / nervous system development / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.403 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 18, 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
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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin 4
B: Contactin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49510
Polymers85,7252
Non-polymers1,7708
Water3,369187
1
A: Contactin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7475
Polymers42,8631
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Contactin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7475
Polymers42,8631
Non-polymers8854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)281.728, 40.431, 95.076
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-162-

TYR

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Components

#1: Protein Contactin 4


Mass: 42862.520 Da / Num. of mol.: 2 / Fragment: Ig 1-4 fragment (UNP residues 25-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn4 / Plasmid: pSGHP1 / Production host: Homo Sapiens (human) / References: UniProt: Q14BL8
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20 mM Na/K phosphate pH 5.8, 10% PEG 3400, 1.2 M 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMar 27, 2009
MARMOSAIC 225 mm CCD2CCDApr 11, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock monochromatorSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40236 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.494.10.5481,281.1
2.49-2.595.40.5041,291.9
2.59-2.77.10.481,297.6
2.7-2.858.90.3681,299.5
2.85-3.0210.30.291,299.9
3.02-3.26110.2151,2100
3.26-3.58110.1641,2100
3.58-4.1110.1451,2100
4.1-5.1710.90.1141,2100
5.17-5010.50.0871,299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.67
Highest resolutionLowest resolution
Rotation2.5 Å45.15 Å
Translation2.5 Å45.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
DPSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→37.172 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0.07 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 1886 4.97 %
Rwork0.197 --
obs0.1997 37921 91.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.885 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso mean: 78.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.457 Å20 Å2-2.688 Å2
2--11.965 Å20 Å2
3----11.508 Å2
Refinement stepCycle: LAST / Resolution: 2.403→37.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5984 0 112 187 6283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056253
X-RAY DIFFRACTIONf_angle_d0.9328478
X-RAY DIFFRACTIONf_dihedral_angle_d17.3032330
X-RAY DIFFRACTIONf_chiral_restr0.06941
X-RAY DIFFRACTIONf_plane_restr0.0051099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.46790.30971030.25581914X-RAY DIFFRACTION65
2.4679-2.54050.30471200.25432274X-RAY DIFFRACTION75
2.5405-2.62250.33561260.25142475X-RAY DIFFRACTION83
2.6225-2.71620.34881350.24832655X-RAY DIFFRACTION87
2.7162-2.82490.28031420.23152711X-RAY DIFFRACTION92
2.8249-2.95340.31941480.23062842X-RAY DIFFRACTION94
2.9534-3.10910.28391540.22612903X-RAY DIFFRACTION96
3.1091-3.30380.28321530.21812927X-RAY DIFFRACTION97
3.3038-3.55860.25881570.20952991X-RAY DIFFRACTION98
3.5586-3.91640.23751580.19383016X-RAY DIFFRACTION100
3.9164-4.48230.2341620.15723070X-RAY DIFFRACTION100
4.4823-5.64410.18911610.14533072X-RAY DIFFRACTION100
5.6441-37.17660.21461670.17433185X-RAY DIFFRACTION99
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)
1-0.1593-0.5756-0.84130.66320.64582.22750.36670.05090.4521-0.05620.3197-0.2397-0.2384-1.4982-0.42480.63070.39630.11821.36460.27540.358947.19692.1194-10.7233
21.13540.1731-1.52010.59470.85090.44850.14740.26830.57020.28580.2150.5662-0.4806-1.8589-0.26550.64560.35370.13151.88680.38850.506440.2451-0.2946-7.3657
31.4345-0.6093-0.97171.64630.1512.13730.10640.31350.1584-0.1675-0.0148-0.0697-0.2483-0.2325-0.11530.19870.00010.0274-0.00990.06030.142959.4472-12.618826.7324
41.2738-0.5429-0.70341.5680.9829-0.5920.20140.3992-0.3212-0.88720.16480.23751.1174-0.9565-0.2410.8721-0.3236-0.13850.64150.1250.235955.7086-14.9748-22.1132
5-0.34830.0363-0.370.3557-0.13051.668-0.10160.6191-0.4756-0.46520.08420.29310.1107-0.1056-0.06590.4352-0.016-0.34050.6154-0.10910.758625.2634-24.165413.9504
60.1240.1233-0.15620.2538-0.05980.199-0.11320.297-0.466-0.16860.53170.34630.081-0.9602-0.5370.72970.1044-0.28431.25450.01341.1477-6.1196-11.35194.584
70.47810.3952-0.45520.62720.23010.7974-0.037-0.37490.27840.0540.12420.2105-0.1284-0.2641-0.14920.19010.2424-0.16751.0721-0.11130.7544-3.42545.346320.3651
8-1.10910.71780.74191.4991.06963.24320.231-0.2605-0.2366-0.0608-0.22280.50570.2971-1.0281-0.0130.2261-0.08720.00420.51580.03210.474535.2781-20.80536.5824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 22:64A22 - 64
2X-RAY DIFFRACTION2(chain A and resid 65:118)A65 - 118
3X-RAY DIFFRACTION3(chain A and resid 119:314)A119 - 314
4X-RAY DIFFRACTION4(chain A and resid 315:403)A315 - 403
5X-RAY DIFFRACTION5(chain B and resid 22:119)B22 - 119
6X-RAY DIFFRACTION6(chain B and resid 120:129)B120 - 129
7X-RAY DIFFRACTION7(chain B and resid 130:312)B130 - 312
8X-RAY DIFFRACTION8(chain B and resid 313:404)B313 - 404

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