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Yorodumi- PDB-8avi: Crystal structure of IsdG from Bacillus cereus in complex with heme -
+Open data
-Basic information
Entry | Database: PDB / ID: 8avi | ||||||
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Title | Crystal structure of IsdG from Bacillus cereus in complex with heme | ||||||
Components | Heme-degrading monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / HEME DEGRADATION / MONOOXYGENASE | ||||||
Function / homology | Function and homology information iron import into cell / heme oxygenase (biliverdin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Andersen, H.K. / Hammerstad, M. / Hersleth, H.-P. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Antioxidants / Year: 2023 Title: Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Authors: Hammerstad, M. / Rugtveit, A.K. / Dahlen, S. / Andersen, H.K. / Hersleth, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8avi.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8avi.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 8avi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/8avi ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avi | HTTPS FTP |
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-Related structure data
Related structure data | 8avhSC 8c16C 8c3mC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12049.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) Strain: ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711 Gene: isdG, BC_4542 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q812Q3, heme oxygenase (staphylobilin-producing) |
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-Non-polymers , 5 types, 47 molecules
#2: Chemical | #3: Chemical | ChemComp-PGO / | #4: Chemical | ChemComp-BU1 / | #5: Chemical | ChemComp-PDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18 mg/mL IsdaG (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0. ...Details: 18 mg/mL IsdaG (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.969998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969998 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.04 Å / Num. obs: 16227 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1200 / CC1/2: 0.579 / Rpim(I) all: 0.498 / Rrim(I) all: 1.313 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AVH Resolution: 2→44.04 Å / SU ML: 0.2365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5781 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.04 Å
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Refine LS restraints |
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LS refinement shell |
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