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- PDB-2wim: Crystal structure of NCAM2 IG1-3 -

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Basic information

Entry
Database: PDB / ID: 2wim
TitleCrystal structure of NCAM2 IG1-3
ComponentsNEURAL CELL ADHESION MOLECULE 2
KeywordsCELL ADHESION / CELL MEMBRANE / TRANSMEMBRANE / 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: 3 Å
AuthorsKulahin, N. / Kristensen, O. / Rasmussen, K. / Kastrup, J. / Berezin, V. / Bock, E. / Walmod, P. / 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
DepositionMay 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 25, 2018Group: 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 / citation / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn
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 / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE 2
B: NEURAL CELL ADHESION MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9776
Polymers65,2732
Non-polymers7044
Water55831
1
A: NEURAL CELL ADHESION MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1194
Polymers32,6371
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEURAL CELL ADHESION MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8582
Polymers32,6371
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.390, 106.780, 188.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9962, -0.06058, 0.06181), (-0.01405, -0.5915, -0.8062), (0.08539, -0.804, 0.5884)
Vector: 16.1, 42.7, 20.44)

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Components

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


Mass: 32636.561 Da / Num. of mol.: 2 / Fragment: IGI-III, RESIDUES 19-301
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.93 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 4.5
Details: 14 % PEG-3350, 20 MM CACL2, 0.1 M CITRIC ACID PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9755
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 3→24.57 Å / Num. obs: 15703 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 76.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.6
Reflection shellResolution: 3→3.08 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.8 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.574 Å / SU ML: 2.21 / σ(F): 0.05 / Phase error: 32.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 752 5 %
Rwork0.2133 --
obs0.2171 14986 91.89 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.561 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 96.581 Å2
Baniso -1Baniso -2Baniso -3
1--17.6169 Å20 Å2-0 Å2
2--38.4026 Å2-0 Å2
3----20.7857 Å2
Refinement stepCycle: LAST / Resolution: 3→24.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 43 31 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064323
X-RAY DIFFRACTIONf_angle_d0.9785841
X-RAY DIFFRACTIONf_dihedral_angle_d18.4921611
X-RAY DIFFRACTIONf_chiral_restr0.059664
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.23130.35641310.24922603X-RAY DIFFRACTION85
3.2313-3.55560.32811490.23352773X-RAY DIFFRACTION91
3.5556-4.06810.34811570.21682849X-RAY DIFFRACTION94
4.0681-5.11770.21461550.17242994X-RAY DIFFRACTION96
5.1177-24.57510.2941600.22773015X-RAY DIFFRACTION92

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