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- PDB-2jll: Crystal structure of NCAM2 IgIV-FN3II -

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Basic information

Entry
Database: PDB / ID: 2jll
TitleCrystal structure of NCAM2 IgIV-FN3II
ComponentsNEURAL CELL ADHESION MOLECULE 2
KeywordsCELL ADHESION / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN SUPERFAMILY / TRANSMEMBRANE / PHOSPHOPROTEIN / NEURAL / MEMBRANE / GLYCOPROTEIN / CELL MEMBRANE
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: 2.3 Å
AuthorsKulahin, N. / Rasmussen, K. / Kristensen, O. / 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
DepositionSep 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7137
Polymers43,6961
Non-polymers1,0176
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.740, 33.800, 97.670
Angle α, β, γ (deg.)90.00, 98.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2090-

HOH

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Components

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


Mass: 43696.059 Da / Num. of mol.: 1 / Fragment: IGIV-FN3II, RESIDUES 301-689
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / 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.: 4
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.48 Å3/Da / Density % sol: 50.39 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M HEPES PH6.5, 14% PEG10000, 0.2M CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→19.79 Å / Num. obs: 38513 / % possible obs: 90.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 43.77 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.791 Å / SU ML: 0.39 / σ(F): 0.94 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1987 5.2 %
Rwork0.2156 --
obs0.2183 38513 90.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.61 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 51.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.9794 Å20 Å2-6.5728 Å2
2---3.0432 Å20 Å2
3---0.0638 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 63 147 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d03177
X-RAY DIFFRACTIONf_angle_d0.924302
X-RAY DIFFRACTIONf_dihedral_angle_d15.321178
X-RAY DIFFRACTIONf_chiral_restr0.05476
X-RAY DIFFRACTIONf_plane_restr0549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.34311540.31592633X-RAY DIFFRACTION92
2.3575-2.42110.3661470.31272698X-RAY DIFFRACTION91
2.4211-2.49220.32471260.29722635X-RAY DIFFRACTION94
2.4922-2.57250.35831350.28042694X-RAY DIFFRACTION91
2.5725-2.66420.33781570.27432617X-RAY DIFFRACTION92
2.6642-2.77060.27881520.27132631X-RAY DIFFRACTION91
2.7706-2.89630.31971320.24852625X-RAY DIFFRACTION91
2.8963-3.04850.32921440.24692654X-RAY DIFFRACTION90
3.0485-3.23870.30181680.2362549X-RAY DIFFRACTION91
3.2387-3.48760.27081300.20612617X-RAY DIFFRACTION90
3.4876-3.83620.26051500.19592583X-RAY DIFFRACTION90
3.8362-4.38610.21191550.1712557X-RAY DIFFRACTION90
4.3861-5.50620.18581130.14832604X-RAY DIFFRACTION89
5.5062-19.79210.21591240.17962429X-RAY DIFFRACTION84

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