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Yorodumi- PDB-2zdp: Crystal structure of IsdI in complex with Cobalt protoporphyrin IX -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zdp | ||||||
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Title | Crystal structure of IsdI in complex with Cobalt protoporphyrin IX | ||||||
Components | Heme-degrading monooxygenase isdI | ||||||
Keywords | OXIDOREDUCTASE / ruffling / beta-barrel / cobalt protoporphyrin IX / Cytoplasm / Heme / Iron / Metal-binding / Monooxygenase | ||||||
Function / homology | Function and homology information heme oxygenase (staphylobilin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lee, W.C. / Reniere, M.L. / Skaar, E.P. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus Authors: Lee, W.C. / Reniere, M.L. / Skaar, E.P. / Murphy, M.E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zdp.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zdp.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zdp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2zdp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2zdp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2zdp_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zdp ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zdp | HTTPS FTP |
-Related structure data
Related structure data | 2zdoC 1xbwS C: citing same article (ref.) 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
#1: Protein | Mass: 13015.394 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: isdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7A827, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→56 Å / Num. obs: 39272 / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.323 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XBW Resolution: 1.5→55.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.108 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.929 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→55.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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