+Open data
-Basic information
Entry | Database: PDB / ID: 1o9j | ||||||
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Title | The X-ray crystal structure of eta-crystallin | ||||||
Components | ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1 | ||||||
Keywords | OXIDOREDUCTASE / ALDH / EYE-LENS PROTEIN / ETA-CRYSTALLIN | ||||||
Function / homology | Function and homology information ethanol catabolic process / retinal metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / NAD binding / structural molecule activity / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ELEPHANTULUS EDWARDII (Cape elephant shrew) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Purkiss, A.G. / Van Montfort, R. / Wistow, G. / Slingsby, C. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal Structure of Eta-Crystallin: Adaptation of a Class 1 Aldehyde Dehydrogenase for a New Role in the Eye Lens Authors: Bateman, O.A. / Purkiss, A.G. / Van Montfort, R. / Slingsby, C. / Graham, C. / Wistow, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9j.cif.gz | 382.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9j.ent.gz | 312.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9j_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1o9j_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1o9j_validation.xml.gz | 70.8 KB | Display | |
Data in CIF | 1o9j_validation.cif.gz | 98.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9j ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9j | HTTPS FTP |
-Related structure data
Related structure data | 1bxsS 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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-Components
#1: Protein | Mass: 54599.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: NAD COFACTOR PRESENT Source: (gene. exp.) ELEPHANTULUS EDWARDII (Cape elephant shrew) Tissue: LENS / Organ: EYE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q28399, aldehyde dehydrogenase (NAD+) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-DTT / | #4: Chemical | ChemComp-DTU / ( | #5: Water | ChemComp-HOH / | Compound details | MAJOR COMPONENT OF THE EYE OF ELEPHANT SHREWS. THIS ANIMAL HAS BOTH A LENS- AND A NON-LENS CLASS-1 ...MAJOR COMPONENT OF THE EYE OF ELEPHANT SHREWS. THIS ANIMAL HAS BOTH A LENS- AND A NON-LENS CLASS-1 ALDEHYDE DEHYDROGEN | |
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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: 4.2 Å3/Da / Density % sol: 70.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 25 MM BIS-TRIS-PROPANE PH 7.5, APPROXIMATELY 14% PEG 6,000. | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.6 Å / Num. obs: 67543 / % possible obs: 96.5 % / Observed criterion σ(I): 4 / Redundancy: 2.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.2 / % possible all: 94.7 |
Reflection | *PLUS Num. measured all: 159192 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 94.7 % / Num. unique obs: 8412 / Num. measured obs: 20625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXS Resolution: 2.4→41.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / SU B: 9.317 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 1.814 / ESU R Free: 0.312 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→41.52 Å
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Refine LS restraints |
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