+Open data
-Basic information
Entry | Database: PDB / ID: 1bva | ||||||
---|---|---|---|---|---|---|---|
Title | MANGANESE BINDING MUTANT IN CYTOCHROME C PEROXIDASE | ||||||
Components | PROTEIN (CYTOCHROME C PEROXIDASE) | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / METALLOENZYME / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Wilcox, S.K. / Mcree, D.E. / Goodin, D.B. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Rational design of a functional metalloenzyme: introduction of a site for manganese binding and oxidation into a heme peroxidase. Authors: Wilcox, S.K. / Putnam, C.D. / Sastry, M. / Blankenship, J. / Chazin, W.J. / McRee, D.E. / Goodin, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bva.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bva.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bva_validation.pdf.gz | 476.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bva_full_validation.pdf.gz | 483.1 KB | Display | |
Data in XML | 1bva_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1bva_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bva ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bva | HTTPS FTP |
-Related structure data
Related structure data | 1ccgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33635.371 Da / Num. of mol.: 1 / Mutation: D37E,P44D,V45D Source method: isolated from a genetically manipulated source Details: CRYSTAL FORM MKTBY Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BL21 (DE3) / Description: MUTATION TO BIND MANGANESE / Cellular location: CYTOPLASM / Gene: CCP (MKT) / Organelle: MITOCHONDRIA / Plasmid: PT7CCP / Species (production host): Escherichia coli / Gene (production host): CCP (MKT) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00431, cytochrome-c peroxidase |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Sequence details | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM 2CYP BY STRAIN RELATED SUBSTITUTIONS OF THR 53 WITH ILE, ...THIS CYTOCHROME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % Description: A 100K STRUCTURE OF 1CCG WAS USED INITIALLY BECAUSE IT HAD THE MOST SIMILAR UNIT CELL. THE APPROPRIATE AMINO ACID IDENTITIES WERE CHANGED. | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: 20% MPD, 35 MM PHOSPHATE, PH 6.0, 5 MM MNSO4. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→15 Å / Num. obs: 26232 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.89→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.39 / Rsym value: 0.14 / % possible all: 42 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CCG Resolution: 1.89→10 Å / Num. parameters: 10891 / Num. restraintsaints: 9784 / σ(F): 2
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / Rfactor all: 0.179 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.7 |