+Open data
-Basic information
Entry | Database: PDB / ID: 1lr6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of V45Y mutant of cytochrome b5 | ||||||
Components | cytochrome b5 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME B5 / TRYPSIN-SOLUBILIZED FRAGMENT / MUTANT V45Y | ||||||
Function / homology | Function and homology information Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Gan, J.-H. / Wu, J. / Wang, Z.-Q. / Wang, Y.-H. / Huang, Z.-X. / Xia, Z.-X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of V45E and V45Y mutants and structure comparison of a variety of cytochrome b5 mutants. Authors: Gan, J.H. / Wu, J. / Wang, Z.Q. / Wang, Y.H. / Huang, Z.X. / Xia, Z.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lr6.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lr6.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lr6_validation.pdf.gz | 800.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lr6_full_validation.pdf.gz | 800.6 KB | Display | |
Data in XML | 1lr6_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1lr6_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lr6 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lr6 | HTTPS FTP |
-Related structure data
Related structure data | 1lqxC 1ehbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9539.423 Da / Num. of mol.: 1 / Fragment: trypsin-solubilized fragment of cytochrome b5 / Mutation: V45Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: liver / Plasmid: pU19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00171 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PHOSPHATE BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→22.82 Å / Num. obs: 7563 / % possible obs: 93.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.1 / % possible all: 76.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 76.3 % / Rmerge(I) obs: 0.194 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1EHB Resolution: 1.9→22.82 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.6757 Å2 / ksol: 0.402579 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→22.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor all: 0.196 / Rfactor obs: 0.191 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.274 / Rfactor Rwork: 0.289 |