+Open data
-Basic information
Entry | Database: PDB / ID: 2uz2 | ||||||
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Title | Crystal structure of Xenavidin | ||||||
Components | XENAVIDIN | ||||||
Keywords | GLYCOPROTEIN / BETA-BARREL / BIOTIN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | XENOPUS TROPICALIS (tropical clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å | ||||||
Authors | Helppolainen, S.H. / Maatta, J.A.E. / Airenne, T.T. / Johnson, M.S. / Kulomaa, M.S. / Nordlund, H.R. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2009 Title: Structural and Functional Characteristics of Xenavidin, the First Frog Avidin from Xenopus Tropicalis. Authors: Maatta, J.A.E. / Helppolainen, S.H. / Hytonen, V.P. / Johnson, M.S. / Kulomaa, M.S. / Airenne, T.T. / Nordlund, H.R. | ||||||
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 "DA" 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 | 2uz2.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uz2.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 2uz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uz2 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uz2 | HTTPS FTP |
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-Related 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: (-0.99999, -0.00242, 0.00337), Vector: |
-Components
#1: Protein | Mass: 14887.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS TROPICALIS (tropical clawed frog) Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A7YYL1*PLUS #2: Chemical | ChemComp-ACT / | #3: Chemical | ChemComp-BTN / | #4: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.08 % Description: ARPWARP, STARTING FROM EXISTING MODEL, WAS USED TO BUILD THE INITIAL MODEL. THE EXISTING MODEL WAS BUILT USING AN UNPUBLISHED DATA SET COLLECTED AT THE MAX-LAB BEAM LINE I911 IN JUNE ...Description: ARPWARP, STARTING FROM EXISTING MODEL, WAS USED TO BUILD THE INITIAL MODEL. THE EXISTING MODEL WAS BUILT USING AN UNPUBLISHED DATA SET COLLECTED AT THE MAX-LAB BEAM LINE I911 IN JUNE 2006 AND IS RELATED TO PDB ENTRY 2UYW. |
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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: 1.7→25 Å / Num. obs: 37060 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.491 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.42 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 8.595 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.67 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.523 / SU ML: 0.059 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: 5.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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