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- PDB-1cfb: CRYSTAL STRUCTURE OF TANDEM TYPE III FIBRONECTIN DOMAINS FROM DRO... -

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Entry
Database: PDB / ID: 1cfb
TitleCRYSTAL STRUCTURE OF TANDEM TYPE III FIBRONECTIN DOMAINS FROM DROSOPHILA NEUROGLIAN AT 2.0 ANGSTROMS
ComponentsDROSOPHILA NEUROGLIAN
KeywordsNEURAL ADHESION MOLECULE
Function / homology
Function and homology information


pleated septate junction / central complex development / female courtship behavior / regulation of tube size, open tracheal system / imaginal disc morphogenesis / melanotic encapsulation of foreign target / regulation of female receptivity / cell adhesion involved in heart morphogenesis / septate junction / septate junction assembly ...pleated septate junction / central complex development / female courtship behavior / regulation of tube size, open tracheal system / imaginal disc morphogenesis / melanotic encapsulation of foreign target / regulation of female receptivity / cell adhesion involved in heart morphogenesis / septate junction / septate junction assembly / Non-integrin membrane-ECM interactions / ECM proteoglycans / establishment of glial blood-brain barrier / HS-GAG biosynthesis / HS-GAG degradation / NCAM1 interactions / Degradation of the extracellular matrix / Signal transduction by L1 / nerve maturation / Glycosaminoglycan-protein linkage region biosynthesis / Integrin cell surface interactions / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Formation of the dystrophin-glycoprotein complex (DGC) / photoreceptor cell axon guidance / mushroom body development / male courtship behavior / axon ensheathment / axon extension / neuron cell-cell adhesion / motor neuron axon guidance / dendrite morphogenesis / lateral plasma membrane / axonogenesis / cell adhesion molecule binding / filopodium / cell-cell adhesion / synapse organization / neuron projection / axon / neuronal cell body / calcium ion binding / dendrite / membrane / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHuber, A.H. / Wang, Y.E. / Bieber, A.J. / Bjorkman, P.J.
Citation
Journal: Neuron / Year: 1994
Title: Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.
Authors: Huber, A.H. / Wang, Y.M. / Bieber, A.J. / Bjorkman, P.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1989
Title: Drosophila Neuroglian: A Member of the Immunoglobulin Superfamily with Extensive Homology to the Vertebrate Neural Adhesion Molecule L1
Authors: Bieber, A.J. / Snow, P.M. / Hortsch, M. / Patel, N.H. / Jacobs, J.R. / Traquina, Z.R. / Schilling, J. / Goodman, C.S.
History
DepositionAug 27, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
Remark 700SHEET THIS STRUCTURE CONTAINS SEVERAL "CLASSIC" AND "WIDE" BETA-BULGES AS DESCRIBED BY J.S. ...SHEET THIS STRUCTURE CONTAINS SEVERAL "CLASSIC" AND "WIDE" BETA-BULGES AS DESCRIBED BY J.S.RICHARDSON, E.D.GETZOFF AND D.C.RICHARDSON IN "THE BETA-BULGE: A COMMON SMALL UNIT OF NONREPETITIVE PROTEIN STRUCTURE, "PROC.NATL.ACAD.SCI. USA, VOL. 75, PP. 2574 - 2578, 1978 RESIDUES TYPE OF BETA-BULGE THR 621, GLY 622 CLASSIC LEU 645, HIS 646 CLASSIC ALA 663, TYR 664 CLASSIC GLU 665, LYS 666 WIDE ASN 719, VAL 720 WIDE ASN 746, PHE 747 WIDE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DROSOPHILA NEUROGLIAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8085
Polymers23,0431
Non-polymers7654
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DROSOPHILA NEUROGLIAN
hetero molecules

A: DROSOPHILA NEUROGLIAN
hetero molecules

A: DROSOPHILA NEUROGLIAN
hetero molecules

A: DROSOPHILA NEUROGLIAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,23220
Polymers92,1744
Non-polymers3,05916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation23_655-z+1,y,x1
Buried area7910 Å2
ΔGint-98 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.800, 241.800, 241.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Atom site foot note1: THE FOLLOWING RESIDUES HAVE SOME POORLY DEFINED SIDE CHAIN ATOMS: LYS 629, LYS 693, GLU 726, LYS 754 AND LYS 789. THESE ATOMS WERE EXCLUDED FROM REFINEMENT AND HAVE BEEN GIVEN AN OCCUPANCY OF 0.00 ...1: THE FOLLOWING RESIDUES HAVE SOME POORLY DEFINED SIDE CHAIN ATOMS: LYS 629, LYS 693, GLU 726, LYS 754 AND LYS 789. THESE ATOMS WERE EXCLUDED FROM REFINEMENT AND HAVE BEEN GIVEN AN OCCUPANCY OF 0.00 AND A B VALUE OF 99.99 IN THIS ENTRY.
2: THIS STRUCTURE CONTAINS SEVERAL "CLASSIC" AND "WIDE" BETA-BULGES AS DESCRIBED BY J.S.RICHARDSON, E.D.GETZOFF AND D.C.RICHARDSON IN "THE BETA-BULGE: A COMMON SMALL UNIT OF NONREPETITIVE PROTEIN ...2: THIS STRUCTURE CONTAINS SEVERAL "CLASSIC" AND "WIDE" BETA-BULGES AS DESCRIBED BY J.S.RICHARDSON, E.D.GETZOFF AND D.C.RICHARDSON IN "THE BETA-BULGE: A COMMON SMALL UNIT OF NONREPETITIVE PROTEIN STRUCTURE, "PROC.NATL.ACAD.SCI. USA, VOL. 75, PP. 2574 - 2578, 1978. RESIDUES TYPE OF BETA-BULGE THR 621, GLY 622 CLASSIC LEU 645, HIS 646 CLASSIC ALA 663, TYR 664 CLASSIC GLU 665, LYS 666 WIDE ASN 719, VAL 720 WIDE ASN 746, PHE 747 WIDE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DROSOPHILA NEUROGLIAN


Mass: 23043.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line: S2 / Gene: POTENTIAL / References: UniProt: P20241

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Sugars , 2 types, 2 molecules

#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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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

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Non-polymers , 3 types, 239 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAT LEAST TWO OF THE PROTEIN'S THREE POTENTIAL N-LINKED GLYCOSYLATION SITES ARE UTILIZED. ELECTRON ...AT LEAST TWO OF THE PROTEIN'S THREE POTENTIAL N-LINKED GLYCOSYLATION SITES ARE UTILIZED. ELECTRON DENSITY IS OBSERVED FOR TWO N-ACETYL-D-GLUCOSAMINE RESIDUES ATTACHED TO ASN 652 AND ONE N-ACETYL-D-GLUCOSAMINE RESIDUE ATTACHED TO ASN 683. THESE RESIDUES WERE INCLUDED IN THE REFINEMENT.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.39 Å3/Da / Density % sol: 80.75 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 Mammonium sulfate1reservoir
2150 mM1reservoirLi2SO4
3100 mMHEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 45766 / Num. measured all: 355936 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å
Details: THE FOLLOWING RESIDUES HAVE SOME POORLY DEFINED SIDE CHAIN ATOMS: LYS 629, LYS 693, GLU 726, LYS 754 AND LYS 789. THESE ATOMS WERE EXCLUDED FROM REFINEMENT AND HAVE BEEN GIVEN AN OCCUPANCY ...Details: THE FOLLOWING RESIDUES HAVE SOME POORLY DEFINED SIDE CHAIN ATOMS: LYS 629, LYS 693, GLU 726, LYS 754 AND LYS 789. THESE ATOMS WERE EXCLUDED FROM REFINEMENT AND HAVE BEEN GIVEN AN OCCUPANCY OF 0.00 AND A B VALUE OF 99.99 IN THIS ENTRY.
RfactorNum. reflection
Rwork0.202 -
obs0.202 45766
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 48 237 1915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor all: 0.202 / Rfactor obs: 0.195 / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.9

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