+Open data
-Basic information
Entry | Database: PDB / ID: 1lc0 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Biliverdin Reductase and the Enzyme-NADH Complex | ||||||
Components | Biliverdin Reductase A | ||||||
Keywords | OXIDOREDUCTASE / biliverdin reductase / tetrapyrrole / bile pigment / heme / bilirubin / NADH | ||||||
Function / homology | Function and homology information biliverdin reductase / biliberdin reductase (NAD+) activity / biliverdin reductase (NADP+) activity / biliverdin reductase [NAD(P)+] activity / Heme degradation / Cytoprotection by HMOX1 / heme catabolic process / nucleotide binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 Å | ||||||
Authors | Whitby, F.G. / Phillips, J.D. / Hill, C.P. / McCoubrey, W. / Maines, M.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex. Authors: Whitby, F.G. / Phillips, J.D. / Hill, C.P. / McCoubrey, W. / Maines, M.D. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE AUTHOR STATES THE PROTEIN WAS EXPRESSED AS AN N-TERMINALLY MODIFIED PROTEIN AS AN AID IN EXPRESSION |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lc0.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lc0.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lc0 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lc0 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33385.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P46844, biliverdin reductase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 2.0 M Na+/K+ phosphate, 100 mM CAPS, 200 mM lithium sulfate (Emerald Screen Wizard-I condition 27), pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 95190 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 |
Reflection shell | Resolution: 1.2→1.21 Å / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 43 Å / Num. obs: 95268 / Num. measured all: 636022 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.2→42.81 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→42.81 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.2→1.21 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 43 Å / Num. reflection Rfree: 1893 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.224 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.299 / Rfactor Rwork: 0.341 |