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- PDB-2om5: N-Terminal Fragment of Human TAX1 -

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Basic information

Entry
Database: PDB / ID: 2om5
TitleN-Terminal Fragment of Human TAX1
ComponentsContactin 2
KeywordsCELL ADHESION / x-ray crystallography / Ig-like C2-type / immunoglobulin superfamily / fibronectin / membrane protein
Function / homology
Function and homology information


establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / dendrite self-avoidance / cell-cell adhesion mediator activity / protein localization to juxtaparanode region of axon / NrCAM interactions / axon initial segment ...establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / dendrite self-avoidance / cell-cell adhesion mediator activity / protein localization to juxtaparanode region of axon / NrCAM interactions / axon initial segment / node of Ranvier / juxtaparanode region of axon / NCAM1 interactions / fat cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane / axon guidance / myelin sheath / postsynaptic membrane / cell adhesion / axon / synapse / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsMoertl, M. / Sonderegger, P. / Diederichs, K. / Welte, W.
CitationJournal: Protein Sci. / Year: 2007
Title: The crystal structure of the ligand-binding module of human TAG-1 suggests a new mode of homophilic interaction
Authors: Mortl, M. / Sonderegger, P. / Diederichs, K. / Welte, W.
History
DepositionJan 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 2


Theoretical massNumber of molelcules
Total (without water)42,2131
Polymers42,2131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.804, 106.916, 161.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Contactin 2 / / TAX1 / Axonin-1 / Axonal glycoprotein TAG-1 / Transient axonal glycoprotein 1 / TAX-1


Mass: 42213.488 Da / Num. of mol.: 1 / Fragment: N TERMINAL FOUR IG DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNTN2, TAG1, TAX / Production host: Escherichia coli (E. coli) / References: UniProt: Q02246

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 20k, potassium chloride, tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.07068
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2004
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07068 Å / Relative weight: 1
ReflectionResolution: 3.07→19.5 Å / Num. all: 7518 / Num. obs: 7518 / % possible obs: 94.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.07→3.26 Å / % possible all: 76.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→19.5 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.867 / SU B: 65.157 / SU ML: 0.503 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 452 6 %RANDOM
Rwork0.235 ---
all0.238 7518 --
obs0.238 7090 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å20 Å2
2---2.19 Å20 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 3.07→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 0 0 2895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.9544039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34923.885139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56215476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21918
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1551.51903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.2722985
X-RAY DIFFRACTIONr_scbond_it0.36431216
X-RAY DIFFRACTIONr_scangle_it0.6314.51054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 3.07 Å / Num. reflection Rwork: 323 / Total num. of bins used: 20
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)
111.1874-2.86853.89194.211.22017.66650.07980.3654-0.27690.37510.13170.1910.9853-0.187-0.21160.358-0.0416-0.03830.06750.05610.1392-2.187-23.915-29.398
23.515-3.9262-2.86957.56232.87315.84550.07220.49170.0772-0.3622-0.6131.4203-0.473-0.69640.54070.0745-0.0154-0.13670.6751-0.20090.6164-36.6370.016-30.068
323.0537-5.51942.14135.9531.69275.2116-0.729-0.75511.02290.96140.3892-0.10560.4720.13540.33980.44820.0777-0.05350.3732-0.22950.3734-27.0287.844-10.553
46.0594-1.55310.48565.0231.67686.154-0.5084-0.63820.23351.49550.2864-0.62980.720.28320.22191.15760.3767-0.36330.362-0.11260.27099.097-20.078-7.79
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 100
2X-RAY DIFFRACTION2A101 - 203
3X-RAY DIFFRACTION3A204 - 295
4X-RAY DIFFRACTION4A296 - 384

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