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- PDB-2xyc: CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I -

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Basic information

Entry
Database: PDB / ID: 2xyc
TitleCRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I
ComponentsNEURAL CELL ADHESION MOLECULE 2
KeywordsCELL ADHESION / GLYCOPROTEIN
Function / homology
Function and homology information


neuron cell-cell adhesion / axonal fasciculation / nuclear body / axon / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neural cell adhesion / 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 V-Type / Fibronectin type-III domain profile. ...Neural cell adhesion / 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 V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / 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
PHOSPHATE ION / Neural cell adhesion molecule 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKulahin, N. / Rasmussen, K.K. / Kristensen, O. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M.
CitationJournal: Structure / Year: 2011
Title: Structural Model and Trans-Interaction of the Entire Ectodomain of the Olfactory Cell Adhesion Molecule.
Authors: Kulahin, N. / Kristensen, O. / Rasmussen, K.K. / Olsen, L. / Rydberg, P. / Vestergaard, B. / Kastrup, J.S. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M.
History
DepositionNov 17, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 23, 2011ID: 2JLK
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6988
Polymers32,5121
Non-polymers1,1877
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.660, 139.660, 47.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

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Components

#1: Protein NEURAL CELL ADHESION MOLECULE 2 / / NCAM2


Mass: 32511.506 Da / Num. of mol.: 1 / Fragment: IGIV-F3I, RESIDUES 301-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: O15394
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.58 Å3/Da / Density % sol: 65.68 % / Description: NONE
Crystal growpH: 7.5
Details: 5MM HEPES PH 7.5, 10% PEG 3350, 0.1M AMMONIUM PHOSPHATE, 10MM TRIMETHYLAMINE HYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.908
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.51→62.46 Å / Num. obs: 16752 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 41.44 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
XIAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→62.458 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 845 5.1 %
Rwork0.1935 --
obs0.1959 16707 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.989 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5311 Å20 Å20 Å2
2--2.5311 Å20 Å2
3----5.0621 Å2
Refinement stepCycle: LAST / Resolution: 2.51→62.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 72 183 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082471
X-RAY DIFFRACTIONf_angle_d1.1573363
X-RAY DIFFRACTIONf_dihedral_angle_d15.387928
X-RAY DIFFRACTIONf_chiral_restr0.076371
X-RAY DIFFRACTIONf_plane_restr0.004429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5094-2.66660.33521560.27592556X-RAY DIFFRACTION100
2.6666-2.87250.32481470.25542581X-RAY DIFFRACTION100
2.8725-3.16150.27911380.19772618X-RAY DIFFRACTION100
3.1615-3.6190.23281450.18062621X-RAY DIFFRACTION100
3.619-4.55930.2161280.172671X-RAY DIFFRACTION100
4.5593-62.47720.19931310.18462815X-RAY DIFFRACTION99

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