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Open data
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Basic information
Entry | Database: PDB / ID: 3qgp | ||||||
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Title | Crystal structure of IsdI in complex with heme and cyanide | ||||||
![]() | Heme-degrading monooxygenase isdI | ||||||
![]() | OXIDOREDUCTASE / Dimeric alpha+beta / barrel | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ukpabi, G.N. / Murphy, M.E.P. | ||||||
![]() | ![]() Title: Heme Ruffling Enables the Catalytic Activity of the Heme Degrading Enzyme IsdI Authors: Takayama, S.J. / Ukpabi, G.N. / Murphy, M.E.P. / Mauk, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lgnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: N315 / Gene: isdI, SA0160 / Production host: ![]() ![]() References: UniProt: Q7A827, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% w/v polyethylene glycol 3350, 0.2 M MgCl2, 0.1 M Bis-Tris, pH 5.5, and flash frozen with a cryoprotectant of 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2008 / Details: Mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97607 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→43.871 Å / Num. all: 25604 / Num. obs: 25604 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rsym value: 0.078 / Net I/σ(I): 16.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LGN Resolution: 1.8→43.871 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.898 / SU B: 2.17 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1233 / SU Rfree: 0.1095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 51.62 Å2 / Biso mean: 17.0882 Å2 / Biso min: 2.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.871 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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