+Open data
-Basic information
Entry | Database: PDB / ID: 4fnh | ||||||
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Title | Crystal structure of IsdI-W66Y in complex with heme | ||||||
Components | Heme-degrading monooxygenase isdI | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta barrel | ||||||
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 subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ukpabi, G.N. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling. Authors: Ukpabi, G. / Takayama, S.J. / Mauk, A.G. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fnh.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fnh.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fnh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4fnh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4fnh_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4fnh_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/4fnh ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fnh | HTTPS FTP |
-Related structure data
Related structure data | 4fniC 3lgnS 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: 12992.358 Da / Num. of mol.: 2 / Mutation: W66Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: N315 / Gene: isdI, SA0160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7A827, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Crystals were grown in a reservoir solution containing 25% w/v polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.0, and flash frozen with a cryoprotectant of 20% ...Details: Crystals were grown in a reservoir solution containing 25% w/v polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.0, and flash frozen with a cryoprotectant of 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97946 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2010 / Details: mirrors |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50.12 Å / Num. all: 24334 / Num. obs: 24334 / Redundancy: 6.6 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LGN Resolution: 1.9→38.33 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.967 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 15.054 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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