[English] 日本語
Yorodumi- PDB-1idq: CRYSTAL STRUCTURE OF NATIVE VANADIUM-CONTAINING CHLOROPEROXIDASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1idq | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF NATIVE VANADIUM-CONTAINING CHLOROPEROXIDASE FROM CURVULARIA INAEQUALIS | ||||||
Components | VANADIUM CHLOROPEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / Two four-helix bundles | ||||||
Function / homology | Function and homology information chloride peroxidase / chloride peroxidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Curvularia inaequalis (fungus) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.03 Å | ||||||
Authors | Messerschmidt, A. / Prade, L. / Wever, R. | ||||||
Citation | Journal: Biol.Chem. / Year: 1997 Title: Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvularia inaequalis by X-ray structures of the native and peroxide form. Authors: Messerschmidt, A. / Prade, L. / Wever, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1idq.cif.gz | 136.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1idq.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1idq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1idq_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1idq_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 1idq_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 1idq_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idq ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idq | HTTPS FTP |
-Related structure data
Related structure data | 1iduC 1vncS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The molecule occurs as monomer |
-Components
#1: Protein | Mass: 67627.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Curvularia inaequalis (fungus) Strain: STRAIN 102.42 FROM CENTRAAL BUREAU VOR SCHIMMELCULTURES (CBS, BAARN, THE NETHERLANDS) References: UniProt: P49053, chloride peroxidase |
---|---|
#2: Chemical | ChemComp-VO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Reservoir: 1.5 M ammonium sulfate, 0.1 M Tris-HCl; Protein drop: 7.5 microliter protein (8.7 mg/ml) in 5 mM Mops and 1 mM Na3VO4 plus 2.5 microliter reservoir solution, pH 8.0, VAPOR ...Details: Reservoir: 1.5 M ammonium sulfate, 0.1 M Tris-HCl; Protein drop: 7.5 microliter protein (8.7 mg/ml) in 5 mM Mops and 1 mM Na3VO4 plus 2.5 microliter reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: HENDRIX-LENTFER / Detector: IMAGE PLATE / Date: Mar 14, 1995 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.031→15.656 Å / Num. all: 46965 / Num. obs: 45791 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 29.01 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.101 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3649 / Rsym value: 0.562 / % possible all: 80.4 |
Reflection | *PLUS Num. measured all: 128746 |
Reflection shell | *PLUS % possible obs: 80.4 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1VNC Resolution: 2.03→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.85 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→8 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.17 | |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|