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Open data
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Basic information
Entry | Database: PDB / ID: 2c1y | ||||||
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Title | Structure of PDI-related Chaperone, Wind mutant-Y55K | ||||||
![]() | WINDBEUTEL PROTEIN | ||||||
![]() | CHAPERONE / WIND / WINDBEUTEL / PDI-DBETA / PDI / PROTEIN DISULFIDE ISOMERASE / PIPE / DORSAL-VENTRAL PATTERNING / WIND MUTANTS / DEVELOPMENTAL PROTEIN / ENDOPLASMIC RETICULUM | ||||||
Function / homology | ![]() 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 / regulation of multicellular organism growth / protein secretion / endomembrane system / endoplasmic reticulum lumen / endoplasmic reticulum / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sevvana, M. / Ma, Q. / Barnewitz, K. / Guo, C. / Soling, H.-D. / Ferrari, D.M. / Sheldrick, G.M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 116.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c0eC ![]() 2c0fC ![]() 2c0gC ![]() 1ovnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28513.531 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | INVOLVED IN DORSOVENTRAL AXIS PATTERNING IN EARLY EMBRYOS. ENGINEERED RESIDUE IN CHAIN A, TYR 55 TO ...INVOLVED IN DORSOVENTR | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.72 % |
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Crystal grow | pH: 8.2 Details: 0.1M TRIS-HCL PH 8.2-8.8 25 MM MGCL2 10% PEG4000 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 22938 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.67 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.83 |
Reflection shell | Resolution: 2.25→2.34 Å / Redundancy: 2.62 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.51 / % possible all: 91.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OVN Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.033 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R Free: 0.229 / 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: 45.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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