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- PDB-5e53: Crystal structure of chicken CNTN1 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 5.0E+53
TitleCrystal structure of chicken CNTN1 FN1-FN3 domains
ComponentsContactin-1
KeywordsCELL ADHESION / Neural cell adhesion molecule / Fibronectin type III domains
Function / homology
Function and homology information


cell-cell adhesion mediator activity / side of membrane / axon guidance / brain development / cell-cell adhesion / axon / 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 ...: / : / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Contactin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.497 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 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-1
B: Contactin-1
C: Contactin-1
D: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,23719
Polymers134,2014
Non-polymers1,03615
Water4,143230
1
A: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7584
Polymers33,5501
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6883
Polymers33,5501
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8275
Polymers33,5501
Non-polymers2764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9657
Polymers33,5501
Non-polymers4156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.484, 49.871, 163.302
Angle α, β, γ (deg.)90.000, 97.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Contactin-1 / Neural cell recognition molecule F11


Mass: 33550.289 Da / Num. of mol.: 4 / Fragment: FN domains 1-3, UNP residues 601-893
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN1 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14781
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
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 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: Jul 12, 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: 2.497→50 Å / Num. obs: 48701 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 44.67 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.035 / Net I/av σ(I): 20.407 / Net I/σ(I): 8.9 / Num. measured all: 171135
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.497-2.594.70.389261.07192.3
2.8-2.917.70.38110151.12762.5
2.91-3.049.60.30711211.05868.4
3.04-3.210.70.25413211.09880.5
3.2-3.411.90.21414841.04389.3
3.4-3.6612.70.18116231.03198.8
3.66-4.03140.14516700.94199.9
4.03-4.6214.30.10516661.03999.9
4.62-5.8114.20.08916911.049100
5.81-5013.40.08617681.02199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å43.51 Å
Translation2.5 Å43.51 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
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7L

5e7l


Resolution: 2.497→43.506 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2355 4.98 %
Rwork0.2048 44902 -
obs0.2069 44684 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 337.16 Å2 / Biso mean: 63.7465 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 2.497→43.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9267 0 75 230 9572
Biso mean--85.46 50.23 -
Num. residues----1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049585
X-RAY DIFFRACTIONf_angle_d0.8413006
X-RAY DIFFRACTIONf_chiral_restr0.0331382
X-RAY DIFFRACTIONf_plane_restr0.0041703
X-RAY DIFFRACTIONf_dihedral_angle_d15.1883527
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4972-2.54820.32691080.26241994210274
2.5482-2.60360.29421280.25842412254088
2.6036-2.66420.36321240.24972491261591
2.6642-2.73080.29981380.24672556269494
2.7308-2.80460.32971330.26572625275896
2.8046-2.88710.34911390.25712621276097
2.8871-2.98030.31581390.25382636277597
2.9803-3.08680.29491450.25462701284698
3.0868-3.21030.28911380.24482680281899
3.2103-3.35640.34411450.23662761290699
3.3564-3.53330.29011410.22272701284299
3.5333-3.75450.24931420.20627442886100
3.7545-4.04420.20291440.197727592903100
4.0442-4.45080.21941450.17427632908100
4.4508-5.0940.18541470.148527812928100
5.094-6.41460.20911460.168627902936100
6.4146-43.51280.18031530.18072887304099
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)
19.67524.10264.48457.34033.16796.45450.26090.1568-0.7828-0.2712-0.30270.49511.275-0.9350.08960.8986-0.1418-0.20290.5162-0.14920.5759-61.684-3.58262.352
28.54091.9766-0.29641.99090.92540.6363-0.2315-0.36470.6255-0.39890.2605-0.072-0.82210.8286-0.02750.8201-0.41690.03960.8138-0.06290.371-28.3174.55277.465
34.53053.2065-4.74682.5426-2.80689.27370.413-1.00520.09140.503-0.60160.18760.06090.23890.15460.428-0.1301-0.03710.6364-0.07480.34963.24416.06557.556
44.0261-0.0943-2.36767.80973.87758.5624-0.18050.3156-0.7073-0.1706-0.0474-0.3790.6860.27220.28040.30570.05250.06920.30630.10920.6518-26.712-23.011-9.758
53.00730.67450.37182.1680.75626.03090.238-0.53691.07420.3427-0.14690.526-0.4909-0.4272-0.09740.3328-0.01550.16140.3202-0.15870.9044-39.596-10.41524.712
62.58030.55812.46660.12370.61472.40410.2979-0.95970.21050.704-0.82480.11750.7247-0.75620.34131.0792-0.48910.16960.9858-0.27590.6025-17.306-7.24558.027
78.38352.1146-1.91846.5865-1.85474.43310.0282-0.6577-0.57560.22470.15650.3296-0.0451-0.9844-0.15360.37690.087-0.05860.6140.04350.3324-70.475.31990.21
84.08490.7963-1.29572.2117-2.23899.607-0.08470.88530.265-0.24210.07370.0977-0.3114-0.15350.03670.36660.0028-0.0960.4487-0.00130.327-57.04719.38457.332
98.56431.10893.70874.5081.24555.5519-0.201-0.248-0.52570.2958-0.0750.10270.23380.05270.24830.30990.05210.06970.36520.05820.3037-78.22614.6925.701
104.55513.15192.84937.98152.70995.53240.47760.1625-0.3481-0.2396-0.15690.60151.0701-0.1511-0.2660.50260.0333-0.15990.226-0.01940.6382-51.808-9.683-19.582
116.11052.0163-0.49622.94040.97792.49870.2098-0.55440.2510.0464-0.1962-0.186-0.40980.4552-0.00410.2937-0.08910.04020.32780.0450.3734-17.4720.931-3.067
125.22152.3728-5.1341.7672-2.14066.69870.6917-0.55650.1610.311-0.46390.0603-0.55850.0995-0.21740.3059-0.09240.01920.46580.00850.425614.1818.655-24.379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 595:692 )A595 - 692
2X-RAY DIFFRACTION2( CHAIN A AND RESID 693:792 )A693 - 792
3X-RAY DIFFRACTION3( CHAIN A AND RESID 793:893 )A793 - 893
4X-RAY DIFFRACTION4( CHAIN B AND RESID 595:692 )B595 - 692
5X-RAY DIFFRACTION5( CHAIN B AND RESID 693:792 )B693 - 792
6X-RAY DIFFRACTION6( CHAIN B AND RESID 793:893 )B793 - 893
7X-RAY DIFFRACTION7( CHAIN C AND RESID 594:692 )C594 - 692
8X-RAY DIFFRACTION8( CHAIN C AND RESID 693:792 )C693 - 792
9X-RAY DIFFRACTION9( CHAIN C AND RESID 793:893 )C793 - 893
10X-RAY DIFFRACTION10( CHAIN D AND RESID 593:692 )D593 - 692
11X-RAY DIFFRACTION11( CHAIN D AND RESID 693:792 )D693 - 792
12X-RAY DIFFRACTION12( CHAIN D AND RESID 793:893 )D793 - 893

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