+Open data
-Basic information
Entry | Database: PDB / ID: 1xlp | ||||||
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Title | Structure of oxidized C73S putidaredoxin from Pseudomonas putida | ||||||
Components | Putidaredoxin | ||||||
Keywords | OXIDOREDUCTASE / [2Fe-2S] / ferredoxin | ||||||
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 / rigid body refinement / Resolution: 2 Å | ||||||
Authors | Sevrioukova, I.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Redox-dependent structural reorganization in putidaredoxin, a vertebrate-type [2Fe-2S] ferredoxin from Pseudomonas putida. Authors: Sevrioukova, I.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xlp.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xlp.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xlp_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 1xlp_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 1xlp_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1xlp_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/1xlp ftp://data.pdbj.org/pub/pdb/validation_reports/xl/1xlp | HTTPS FTP |
-Related structure data
Related structure data | 1xlnC 1xloC 1xlqC 1oqrS 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 on special symmetry positions |
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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, EC: 1.9.3.2 #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: 2.3 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: lithium sulfate, sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 2, 2004 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.36 Å / Num. all: 23647 / Num. obs: 23600 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2190 / Rsym value: 0.674 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 1oqr Resolution: 2→34.36 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat Model / Bsol: 46.6 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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