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Yorodumi- PDB-2ojv: Crystal structure of a ternary complex of goat lactoperoxidase wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ojv | |||||||||
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Title | Crystal structure of a ternary complex of goat lactoperoxidase with cyanide and iodide ions at 2.4 A resolution | |||||||||
Components | Lactoperoxidase | |||||||||
Keywords | METAL BINDING PROTEIN / OXIDOREDUCTASE / cyanide / complex / heam | |||||||||
Function / homology | Function and homology information thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / calcium ion binding / heme binding / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Capra hircus (goat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Singh, A.K. / Singh, N. / Singh, S.B. / Sharma, S. / Kaur, P. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of a ternary complex of goat lactoperoxidase with cyanide and iodide ions at 2.4 A resolution Authors: Singh, A.K. / Singh, N. / Singh, S.B. / Sharma, S. / Kaur, P. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ojv.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ojv.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ojv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ojv_validation.pdf.gz | 750 KB | Display | wwPDB validaton report |
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Full document | 2ojv_full_validation.pdf.gz | 769.3 KB | Display | |
Data in XML | 2ojv_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2ojv_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/2ojv ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2ojv | HTTPS FTP |
-Related structure data
Related structure data | 2gj1 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 67529.781 Da / Num. of mol.: 1 / Fragment: residues 1-595 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS, peroxidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 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 |
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-Non-polymers , 6 types, 418 molecules
#4: Chemical | ChemComp-CA / | ||||
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#5: Chemical | ChemComp-CYN / | ||||
#6: Chemical | ChemComp-CO3 / | ||||
#7: Chemical | ChemComp-IOD / #8: Chemical | ChemComp-HEM / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 100mM Tris-Hcl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54132 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2006 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54132 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→74.54 Å / Num. all: 24962 / Num. obs: 23672 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GJ1 2gj1 Resolution: 2.4→74.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.212 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.607 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→74.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.399→2.461 Å / Total num. of bins used: 20 /
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