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Yorodumi- PDB-1xbw: 1.9A Crystal Structure of the protein isdG from Staphylococcus au... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xbw | ||||||
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Title | 1.9A Crystal Structure of the protein isdG from Staphylococcus aureus aureus, Structural genomics, MCSG | ||||||
Components | hypothetical protein isdG | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / staphylococcus aureus / protein isdG / PSI / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information heme oxygenase (staphylobilin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / monooxygenase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Zhang, R. / Wu, R. / Joachimiak, G. / Schneewind, O. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Staphylococcus aureus IsdG and IsdI, heme-degrading enzymes with structural similarity to monooxygenases. Authors: Wu, R. / Skaar, E.P. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Schneewind, O. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xbw.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xbw.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xbw_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 1xbw_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 1xbw_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1xbw_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/1xbw ftp://data.pdbj.org/pub/pdb/validation_reports/xb/1xbw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | This protein existed as dimer. MolA plus MolB, MolC plus MolD represent two dimers in asymmetric unit |
-Components
#1: Protein | Mass: 12795.507 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: MW2 / Gene: GI:1003130 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NX62 #2: 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: 2.294 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG, 0.1M Bis-tris, 0.2M NH4SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Jul 22, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 66916 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.24 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 4.02 / Num. unique all: 2166 / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→32.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 428884.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0323 Å2 / ksol: 0.406194 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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