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Yorodumi- PDB-3qzn: Staphylococcus aureus IsdA NEAT domain Y166A variant in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qzn | ||||||
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Title | Staphylococcus aureus IsdA NEAT domain Y166A variant in complex with heme | ||||||
Components | Iron-regulated surface determinant protein A | ||||||
Keywords | METAL BINDING PROTEIN / heme / transport / iron / uptake / receptor / cell wall | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Grigg, J.C. / Mao, C.X. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Iron-Coordinating Tyrosine Is a Key Determinant of NEAT Domain Heme Transfer. Authors: Grigg, J.C. / Mao, C.X. / 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 | 3qzn.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qzn.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qzn_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 3qzn_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 3qzn_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 3qzn_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/3qzn ftp://data.pdbj.org/pub/pdb/validation_reports/qz/3qzn | HTTPS FTP |
-Related structure data
Related structure data | 3qzlC 3qzmC 3qzoC 3qzpC 2itfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14554.237 Da / Num. of mol.: 3 / Fragment: UNP Residues 62-184 / Mutation: Y166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: N315 / Gene: frpA, isdA, SA0977, stbA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7A655 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: 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: 3.25 Å3/Da / Density % sol: 62.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2007 / Details: Vertically focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→45 Å / Num. obs: 39286 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.099 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ITF Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.745 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / 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: 60.16 Å2 / Biso mean: 29.916 Å2 / Biso min: 15.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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