+Open data
-Basic information
Entry | Database: PDB / ID: 2c0f | ||||||
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Title | Structure of Wind Y53F mutant | ||||||
Components | WINDBEUTEL PROTEIN | ||||||
Keywords | CHAPERONE / DORSAL-VENTRAL PATTERNING / PDI / PDI-DBETA / PIPE / PROTEIN DISULFIDE ISOMERASE / WIND / WINDBEUTEL / WIND MUTANT / DEVELOPMENTAL PROTEIN / ENDOPLASMIC RETICULUM | ||||||
Function / homology | Function and homology information maternal specification of dorsal/ventral axis, oocyte, soma encoded / dorsal/ventral axis specification / protein folding in endoplasmic reticulum / embryo development ending in birth or egg hatching / protein secretion / regulation of multicellular organism growth / endomembrane system / endoplasmic reticulum lumen / endoplasmic reticulum / protein homodimerization activity Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Sevvana, M. / Ma, Q. / Barnewitz, K. / Guo, C. / Soling, H.-D. / Ferrari, D.M. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structural Elucidation of the Pdi-Related Chaperone Wind with the Help of Mutants. Authors: Sevvana, M. / Biadene, M. / Ma, Q. / Guo, C. / Soling, H.-D. / Sheldrick, G.M. / Ferrari, D.M. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure and Functional Analysis of Drosophila Wind, a Protein-Disulfide Isomerase-Related Protein Authors: Ma, Q. / Guo, C. / Barnewitz, K. / Sheldrick, G.M. / Soeling, H.-D. / Uson, I. / Ferrari, D.M. / Sheldrick, G.M. #2: Journal: J.Biol.Chem. / Year: 2004 Title: Mapping of a Sustrate Binding Site in the Protein Disulfide Isomerase-Related Chaperone Wind Based on Protein Function and Crystal Structure Authors: Barnewitz, K. / Guo, C. / Sevvana, M. / Ma, Q. / Sheldrick, G.M. / Soeling, H.-D. / Ferrari, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c0f.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c0f.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c0f_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 2c0f_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 2c0f_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2c0f_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/2c0f ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c0f | HTTPS FTP |
-Related structure data
Related structure data | 2c0eC 2c0gC 2c1yC 1ovnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28531.523 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: O44342 #2: 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: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | pH: 5.8 Details: PROTEIN: 18.0MG/ML Y53F IN 5MM HEPES PH7.5, 25MM LICL, 0.0025%(V/V) BETA-MERCAPTOETHANOL RESERVOIR: 0.1M MES PH5.8, 50MM LICL, 18%(V/V) PEG 400 CRYO: 0.1M MES PH6.0, 25%(V/V) PEG 400,50MM LICL, pH 5.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8976 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8976 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→20 Å / Num. obs: 22333 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 1.77 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.94 |
Reflection shell | Resolution: 2.28→2.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.26 / % possible all: 88.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OVN Resolution: 2.28→20.24 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.323 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.252 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→20.24 Å
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Refine LS restraints |
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