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- PDB-2vaj: Crystal structure of NCAM2 Ig1 (I4122 cell unit) -

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Basic information

Entry
Database: PDB / ID: 2vaj
TitleCrystal structure of NCAM2 Ig1 (I4122 cell unit)
ComponentsNEURAL CELL ADHESION MOLECULE 2
KeywordsCELL ADHESION / IMMUNOGLOBULIN DOMAIN
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
Neural cell adhesion molecule 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKulahin, N. / Rasmussen, K.K. / Kristensen, O. / Kastrup, J.S. / Navarro-Poulsen, J.-C. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of the Ig1 Domain of the Neural Cell Adhesion Molecule Ncam2 Displays Domain Swapping.
Authors: Rasmussen, K.K. / Kulahin, N. / Kristensen, O. / Poulsen, J.C. / Sigurskjold, B.W. / Kastrup, J.S. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M.
History
DepositionAug 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE 2


Theoretical massNumber of molelcules
Total (without water)10,3651
Polymers10,3651
Non-polymers00
Water1086
1
A: NEURAL CELL ADHESION MOLECULE 2

A: NEURAL CELL ADHESION MOLECULE 2


Theoretical massNumber of molelcules
Total (without water)20,7292
Polymers20,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area12030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)47.279, 47.279, 196.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein NEURAL CELL ADHESION MOLECULE 2 / / NCAM2 / N-CAM 2


Mass: 10364.619 Da / Num. of mol.: 1 / Fragment: IG1, RESIDUES 21-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): KM71H
Production host: PROCHLOROCOCCUS MARINUS SUBSP. PASTORIS (high-light adapted Prochlorococcus)
References: UniProt: O15394
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence details2 AMINO ACID DIFFERENCE BETWEEN THE SEQUENCE OF THE CRYSTALLIZED PROTEIN AND THE DATABASE SEQUENCE

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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: 2.75 Å3/Da / Density % sol: 55.28 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9072
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9072 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.321
ReflectionResolution: 2.7→15 Å / Num. obs: 3356 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NCAM IG1 PDB ENTRY 1EPF, CHAIN A

1epf


Resolution: 2.701→15.197 Å / SU ML: 0.34 / σ(F): 1.97 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 145 4.3 %
Rwork0.2269 --
obs0.2287 3339 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.825 Å2 / ksol: 0.355 e/Å3
Refinement stepCycle: LAST / Resolution: 2.701→15.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 0 6 734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007738
X-RAY DIFFRACTIONf_angle_d1.059999
X-RAY DIFFRACTIONf_dihedral_angle_d20.967270
X-RAY DIFFRACTIONf_chiral_restr0.068118
X-RAY DIFFRACTIONf_plane_restr0.004129

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