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Yorodumi- PDB-1cfb: CRYSTAL STRUCTURE OF TANDEM TYPE III FIBRONECTIN DOMAINS FROM DRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cfb | |||||||||
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Title | CRYSTAL STRUCTURE OF TANDEM TYPE III FIBRONECTIN DOMAINS FROM DROSOPHILA NEUROGLIAN AT 2.0 ANGSTROMS | |||||||||
Components | DROSOPHILA NEUROGLIAN | |||||||||
Keywords | NEURAL ADHESION MOLECULE | |||||||||
Function / homology | Function and homology information pleated septate junction / melanotic encapsulation of foreign target / central complex development / regulation of tube size, open tracheal system / imaginal disc morphogenesis / regulation of female receptivity / cell adhesion involved in heart morphogenesis / septate junction / septate junction assembly / establishment of glial blood-brain barrier ...pleated septate junction / melanotic encapsulation of foreign target / central complex development / regulation of tube size, open tracheal system / imaginal disc morphogenesis / regulation of female receptivity / cell adhesion involved in heart morphogenesis / septate junction / septate junction assembly / establishment of glial blood-brain barrier / nerve maturation / photoreceptor cell axon guidance / mushroom body development / female courtship behavior / male courtship behavior / axon ensheathment / neuron cell-cell adhesion / axon extension / motor neuron axon guidance / dendrite morphogenesis / plasma membrane => GO:0005886 / bicellular tight junction / cell adhesion molecule binding / axonogenesis / filopodium / synapse organization / cell-cell adhesion / axon / dendrite / neuronal cell body / calcium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Huber, 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 |
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Remark 700 | SHEET 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 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cfb.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cfb.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/1cfb ftp://data.pdbj.org/pub/pdb/validation_reports/cf/1cfb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 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 ...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 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 239 molecules
#4: Chemical | ChemComp-SO4 / |
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#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | AT 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 GLYCOSYLAT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.39 Å3/Da / Density % sol: 80.75 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 45766 / Num. measured all: 355936 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Resolution: 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.
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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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 |