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- PDB-3p40: Crystal structure of neurofascin adhesion complex in space group p3221 -

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Basic information

Entry
Database: PDB / ID: 3p40
TitleCrystal structure of neurofascin adhesion complex in space group p3221
ComponentsNeurofascin
KeywordsCELL ADHESION / Ig domains
Function / homology
Function and homology information


paranodal junction / Neurofascin interactions / cell-cell adhesion mediator activity / axon initial segment / peripheral nervous system development / node of Ranvier / Interaction between L1 and Ankyrins / ficolin-1-rich granule membrane / myelination / axon guidance ...paranodal junction / Neurofascin interactions / cell-cell adhesion mediator activity / axon initial segment / peripheral nervous system development / node of Ranvier / Interaction between L1 and Ankyrins / ficolin-1-rich granule membrane / myelination / axon guidance / brain development / cell-cell adhesion / axon / focal adhesion / Neutrophil degranulation / plasma membrane
Similarity search - Function
Neurofascin / Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...Neurofascin / Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Immunoglobulin / Immunoglobulin domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.2 Å
AuthorsLiu, H. / He, X.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Homophilic adhesion mechanism of neurofascin, a member of the l1 family of neural cell adhesion molecules.
Authors: Liu, H. / Focia, P.J. / He, X.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _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.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
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: Neurofascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5062
Polymers45,2851
Non-polymers2211
Water4,594255
1
A: Neurofascin
hetero molecules

A: Neurofascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0134
Polymers90,5702
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2510 Å2
ΔGint1 kcal/mol
Surface area40790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.508, 94.508, 126.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Neurofascin


Mass: 45285.199 Da / Num. of mol.: 1 / Fragment: N-terminal four Ig domains (UNP residues 25-428)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFASC, KIAA0756 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94856
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30%(w/v) PEG400, 0.1 M HEPES, 0.2 lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.54981 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54981 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 12256 / Num. obs: 12195 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1210 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.2→40.92 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1838684.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.316 563 5 %RANDOM
Rwork0.273 ---
all0.296 11235 --
obs0.273 11191 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5836 Å2 / ksol: 0.303892 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.95 Å28.33 Å20 Å2
2---8.95 Å20 Å2
3---17.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.2→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 14 255 3337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d1.23
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 84 4.6 %
Rwork0.348 1751 -
obs-1751 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4ion.paramion.top

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