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- PDB-2haz: Crystal structure of the first fibronectin domain of human NCAM1 -

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Basic information

Entry
Database: PDB / ID: 2haz
TitleCrystal structure of the first fibronectin domain of human NCAM1
ComponentsNeural cell adhesion molecule 1Neural cell adhesion molecule
KeywordsCELL ADHESION / fibronectin type III repeat / FN1 / NCAM / beta sandwich
Function / homology
Function and homology information


regulation of semaphorin-plexin signaling pathway / : / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / type II interferon-mediated signaling pathway / NCAM signaling for neurite out-growth / Signal transduction by L1 / axon guidance ...regulation of semaphorin-plexin signaling pathway / : / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / type II interferon-mediated signaling pathway / NCAM signaling for neurite out-growth / Signal transduction by L1 / axon guidance / Interferon gamma signaling / MAPK cascade / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / membrane => GO:0016020 / cell adhesion / neuron projection / external side of plasma membrane / Golgi membrane / cell surface / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Neural cell adhesion molecule 1 / 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 / Fibronectin type-III domain profile. ...Neural cell adhesion molecule 1 / 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 / 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
Neural cell adhesion molecule 1 / Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSekulic, N. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: A novel alpha-helix in the first fibronectin type III repeat of the neural cell adhesion molecule is critical for N-glycan polysialylation.
Authors: Mendiratta, S.S. / Sekulic, N. / Hernandez-Guzman, F.G. / Close, B.E. / Lavie, A. / Colley, K.J.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neural cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3892
Polymers11,3661
Non-polymers231
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.760, 53.880, 74.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-46-

HOH

21A-77-

HOH

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Components

#1: Protein Neural cell adhesion molecule 1 / Neural cell adhesion molecule / N-CAM 1


Mass: 11365.625 Da / Num. of mol.: 1 / Fragment: first fibronectin type III repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAM1 / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21-DE3 / References: UniProt: P13592, UniProt: P13591*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.3 M Calcium chloride, 17% PEG 3350, 10% PEG 400 (the latter only in the drop), pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. all: 9851 / Num. obs: 9851 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 25.195 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.88
Reflection shellResolution: 1.69→1.79 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 9770 / Num. unique all: 1500 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1UEM

1uem


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.705 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 941 9.7 %RANDOM
Rwork0.212 ---
all0.219 9694 --
obs-9694 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---1.89 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 1 97 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9551109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4325.45533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3615128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.776152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02622
X-RAY DIFFRACTIONr_nbd_refined0.2150.2327
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.271
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3450.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_mcbond_it0.6521.5519
X-RAY DIFFRACTIONr_mcangle_it1.1892836
X-RAY DIFFRACTIONr_scbond_it1.9573312
X-RAY DIFFRACTIONr_scangle_it3.3064.5273
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 68 -
Rwork0.298 640 -
obs-708 100 %

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