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Yorodumi- PDB-1ql3: Structure of the soluble domain of cytochrome c552 from Paracoccu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ql3 | ||||||
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Title | Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state | ||||||
Components | CYTOCHROME C552 | ||||||
Keywords | ELECTRON TRANSPORT PROTEIN (CYTOCHROME) / ELECTRON TRANSFER / REDUCED | ||||||
Function / homology | Function and homology information electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | PARACOCCUS DENITRIFICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å | ||||||
Authors | Harrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States Authors: Harrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ql3.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ql3.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ql3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1ql3 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1ql3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10422.782 Da / Num. of mol.: 4 / Fragment: SOLUBLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: MEMBRANE-BOUNDBiological membrane / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P54820 #2: Chemical | ChemComp-HEC / #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: 2.47 Å3/Da / Density % sol: 49.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9059 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9059 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 80254 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 8.4 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 277074 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: USED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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