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- PDB-1o70: Novel Fold Revealed by the Structure of a FAS1 Domain Pair from t... -

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Basic information

Entry
Database: PDB / ID: 1o70
TitleNovel Fold Revealed by the Structure of a FAS1 Domain Pair from the Insect Cell Adhesion Molecule Fasciclin I
ComponentsFASCICLIN I
KeywordsCELL ADHESION / AXON GUIDANCE / EXTRACELLULAR MODULE / GENETIC DISORDER / CORNEAL DYSTROPHY
Function / homology
Function and homology information


calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / neuron recognition / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane / cell adhesion molecule binding / extracellular matrix organization / extracellular matrix / axon guidance / cell adhesion / extracellular space / plasma membrane
Similarity search - Function
FAS1 domain / FAS1 domain / : / Fasciclin domain / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsClout, N.J. / Tisi, D. / Hohenester, E.
CitationJournal: Structure / Year: 2003
Title: Novel Fold Revealed by the Structure of a Fas1 Domain Pair from the Insect Cell Adhesion Molecule Fasciclin I
Authors: Clout, N.J. / Tisi, D. / Hohenester, E.
History
DepositionOct 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FASCICLIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3026
Polymers36,4931
Non-polymers8095
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.806, 150.806, 150.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein FASCICLIN I / FAS I / FCN


Mass: 36493.141 Da / Num. of mol.: 1 / Fragment: FAS I DOMAINS 3 AND 4, RESIDUES 314-628
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P10674
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNEURAL CELL ADHESION MOLECULE THAT IS EXPRESSED ON DIFFERENT SUBSETS OF AXON BUNDLES IN INSECT EMBRYOS.
Has protein modificationY

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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: 4.07 Å3/Da / Density % sol: 68 %
Crystal growpH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 2.0 M AMMONIUM SULFATE
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.01 Msodium HEPES1droppH7.5
30.1 MTris-HCl1reservoirpH8.5
42.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002 / Details: RH COATED SI MIRROR
RadiationMonochromator: A TRIANGULAR SINGLE CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 17949 / % possible obs: 97.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 4.4
Reflection shellResolution: 2.6→20 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / % possible obs: 97.5 % / Rmerge(I) obs: 0.309

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.259 -9.5 %RANDOM
Rwork0.225 ---
obs0.225 17911 96.3 %-
Displacement parametersBiso mean: 32.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 48 76 2505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 1758 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2

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