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Yorodumi- PDB-1oqr: Crystal structure of C73S mutant of putidaredoxin, a [2Fe-2S] fer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oqr | ||||||
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Title | Crystal structure of C73S mutant of putidaredoxin, a [2Fe-2S] ferredoxin from Pseudomonas putida, at 1.65A resolution | ||||||
Components | Putidaredoxin | ||||||
Keywords | ELECTRON TRANSPORT / electron transfer | ||||||
Function / homology | Function and homology information P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Sevrioukova, I.F. / Garcia, C. / Li, H. / Bhaskar, B. / Poulos, T.L. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 Title: Crystal structure of putidaredoxin, the [2Fe-2S] component of the P450cam monooxygenase system from Pseudomonas putida Authors: Sevrioukova, I.F. / Garcia, C. / Li, H. / Bhaskar, B. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqr.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqr.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1oqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oqr_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 1oqr_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 1oqr_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1oqr_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqr ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqr | HTTPS FTP |
-Related structure data
Related structure data | 1oqqSC 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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Unit cell |
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-Components
#1: Protein | Mass: 11412.846 Da / Num. of mol.: 3 / Mutation: C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMB / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00259 #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 45.53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: lithium sulfate, sodium citrate, dithiothreitol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 2002 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 181573 / Num. obs: 180222 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1996 / Rsym value: 0.618 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 1.67 Å / Num. obs: 39004 / % possible obs: 96.7 % / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: putidaredoxin C73S/C85S mutant, PDB ID code 1OQQ Resolution: 1.65→27.65 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.0092 Å2 / ksol: 0.400588 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→27.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.67 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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