+Open data
-Basic information
Entry | Database: PDB / ID: 2jgs | ||||||
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Title | Circular permutant of avidin | ||||||
Components | CIRCULAR PERMUTANT OF AVIDIN | ||||||
Keywords | BIOTIN-BINDING PROTEIN / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Maatta, J.A.E. / Hytonen, V.P. / Airenne, T.T. / Niskanen, E. / Johnson, M.S. / Kulomaa, M.S. / Nordlund, H.R. | ||||||
Citation | Journal: Chembiochem / Year: 2008 Title: Rational Modification of Ligand-Binding Preference of Avidin by Circular Permutation and Mutagenesis. Authors: Maatta, J.A.E. / Airenne, T.T. / Nordlund, H.R. / Janis, J. / Paldanius, T.A. / Vainiotalo, P. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "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. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 | 2jgs.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgs.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jgs_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
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Full document | 2jgs_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 2jgs_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 2jgs_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgs ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgs | HTTPS FTP |
-Related structure data
Related structure data | 2aviS 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:
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-Components
#1: Protein | Mass: 14309.104 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02701*PLUS #2: Chemical | ChemComp-BTN / #3: Water | ChemComp-HOH / | Sequence details | THE STRUCTURE DEPOSITED IS A CIRCULAR PERMUTANT (ARTIFICIAL LOCATION OF N- AND C-TERMINI & SHORT ...THE STRUCTURE DEPOSITED IS A CIRCULAR PERMUTANT (ARTIFICIAL | |
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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: 2.21 Å3/Da / Density % sol: 43.95 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 36425 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AVI Resolution: 1.9→70.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.01 / SU ML: 0.135 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→70.89 Å
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