+Open data
-Basic information
Entry | Database: PDB / ID: 1vyo | ||||||
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Title | Crystal structure of avidin | ||||||
Components | AVIDIN | ||||||
Keywords | GLYCOPROTEIN / BIOTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Airenne, T.T. / Johnson, M.S. / Salminen, T.A. | ||||||
Citation | Journal: Chem.Biol. / Year: 2006 Title: Binding Properties of Haba-Type Azo Derivatives to Avidin and Avidin-Related Protein 4. Authors: Repo, S. / Paldanius, T.A. / Hytonen, V.P. / Nyholm, T.K. / Halling, K.K. / Huuskonen, J. / Pentikainen, O.T. / Rissanen, K. / Slotte, J.P. / Airenne, T.T. / Salminen, T.A. / Kulomaa, M.S. / Johnson, M.S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vyo.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vyo.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vyo_validation.pdf.gz | 387.8 KB | Display | wwPDB validaton report |
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Full document | 1vyo_full_validation.pdf.gz | 391.2 KB | Display | |
Data in XML | 1vyo_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1vyo_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/1vyo ftp://data.pdbj.org/pub/pdb/validation_reports/vy/1vyo | HTTPS FTP |
-Related structure data
Related structure data | 1avdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.2391, 0.971, 0.0016), Vector: |
-Components
#1: Protein | Mass: 14361.149 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02701 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Compound details | FUNCTION: THE BIOLOGICAL FUNCTION OF AVIDIN IS NOT KNOWN. FORMS A STRONG NON-COVALENT SPECIFIC ...FUNCTION: THE BIOLOGICAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Equal volumes (1 ul) of protein (0.5 mg/ml) in 50 mM Na acetate (pH 4) + 20 mM NaCl and well solution of 0.1 M MES (pH 6.6) + 24% PEG 8000 + 0.2 M Mg acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.804 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.804 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→20 Å / Num. obs: 41811 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.48→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AVD Resolution: 1.48→19.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.213 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PEPTIDE BONDS BETWEEN RESIDUES A41 AND A42 AND BETWEEN B41 AND B42 HAVE BEEN DETERMINED TO BE CIS- BONDS. THESE RESIDUES ARE NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PEPTIDE BONDS BETWEEN RESIDUES A41 AND A42 AND BETWEEN B41 AND B42 HAVE BEEN DETERMINED TO BE CIS- BONDS. THESE RESIDUES ARE NOT EXPECTED TO ADOPT THE CIS- CONFORMATION. THIS IS DUE TO THE POOR ELECTRON DENSITY IN THESE REGIONS OF THE ELECTRON DENSITY MAP. RESIDUES 34-46 OF BOTH CHAINS FORM LOOPS WITH TWO ALTERNATE CONFORMATIONS. BOTH ALTERNATE CONFORMATIONS CAN BE DETERMINED FOR RESIDUES 34-36 AND 42-46, BUT DUE TO POOR ELECTRON DENSITY RESIDUES 37-41 CAN BE ASSIGNED ONLY A SINGLE CONFORMATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→19.1 Å
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