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- PDB-3qzn: Staphylococcus aureus IsdA NEAT domain Y166A variant in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qzn | ||||||
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Title | Staphylococcus aureus IsdA NEAT domain Y166A variant in complex with heme | ||||||
![]() | Iron-regulated surface determinant protein A | ||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Grigg, J.C. / Mao, C.X. / Murphy, M.E.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qzlC ![]() 3qzmC ![]() 3qzoC ![]() 3qzpC ![]() 2itfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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.) ![]() ![]() ![]() Strain: N315 / Gene: frpA, isdA, SA0977, stbA / Plasmid: pET28a / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-GOL / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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