[English] 日本語
Yorodumi- PDB-2j18: Chloroperoxidase mixture of ferric and ferrous states (low dose d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j18 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Chloroperoxidase mixture of ferric and ferrous states (low dose data set) | ||||||||||||
Components | CHLOROPEROXIDASEChloride peroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN / METAL-BINDING / IRON / HEME / CHLORIDE / MANGANESE / PEROXIDASE | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | CALDARIOMYCES FUMAGO (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Beitlich, T. / Kuhnel, K. / Schulze-Briese, C. / Shoeman, R.L. / Schlichting, I. | ||||||||||||
Citation | Journal: J.Synchrotron Radiat. / Year: 2007 Title: Cryoradiolytic Reduction of Crystalline Heme Proteins: Analysis by Uv-Vis Spectroscopy and X-Ray Crystallography Authors: Beitlich, T. / Kuhnel, K. / Schulze-Briese, C. / Shoeman, R.L. / Schlichting, I. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j18.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j18.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 2j18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/2j18 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/2j18 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2j19C 1cpoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32746.885 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CALDARIOMYCES FUMAGO (fungus) / Production host: CALDARIOMYCES FUMAGO (fungus) / References: UniProt: P04963, chloride peroxidase |
---|
-Sugars , 5 types, 13 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose |
#7: Sugar | ChemComp-NAG / |
#8: Sugar | ChemComp-MAN / |
-Non-polymers , 4 types, 365 molecules
#5: Chemical | ChemComp-MN / | ||
---|---|---|---|
#6: Chemical | ChemComp-HEM / | ||
#9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYZES PEROXIDATIVE HALOGENATIONS INVOLVED IN THE BIOSYNTHESIS OF CLARDARIOMYCIN (2,2-DICHLORO- ...CATALYZES PEROXIDATI |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 11 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % |
---|---|
Crystal grow | pH: 3.4 Details: 50MM KBR, 20% PEG3000, 0.1 M SODIUM CITRATE PH3.4, pH 3.40 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9761 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9761 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 185512 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.3 / % possible all: 95.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CPO Resolution: 1.75→19.75 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.829 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS AN ELONGATED DENSITY ABOVE THE HEME, WHICH WAS MODELLED AS A SINGLE WATER MOLECULE IN TWO POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|