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Yorodumi- PDB-3m97: Structure of the soluble domain of cytochrome c552 with its flexi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m97 | ||||||
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Title | Structure of the soluble domain of cytochrome c552 with its flexible linker segment from Paracoccus denitrificans | ||||||
Components | Cytochrome c-552 | ||||||
Keywords | ELECTRON TRANSPORT / Electron transport chain (cytochrome) / Electron transfer / P. denitrificans / electron donor / Cell membrane / Heme / Iron / Membrane / Metal-binding / Transmembrane / Transport | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.332 Å | ||||||
Authors | Rajendran, C. / Ermler, U. / Ludwig, B. / Michel, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structure at 1.5 A resolution of cytochrome c(552) with its flexible linker segment, a membrane-anchored protein from Paracoccus denitrificans. Authors: Rajendran, C. / Ermler, U. / 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 | 3m97.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m97.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 3m97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m97 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m97 | HTTPS FTP |
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-Related structure data
Related structure data | 1ql4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14515.024 Da / Num. of mol.: 1 Fragment: soluble domain with flexible linker segment (UNP residues 38-176) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: cycM / Production host: Escherichia coli (E. coli) / References: UniProt: P54820 | ||
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#2: Chemical | ChemComp-HEC / | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 % PEG 550 MME, 0.1 M Zinc sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA |
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Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.33→29.13 Å / Num. all: 31610 / Num. obs: 31610 / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 |
Reflection shell | Highest resolution: 1.33 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 29.79 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QL4 Resolution: 1.332→29.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.21 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.768 Å2
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Refinement step | Cycle: LAST / Resolution: 1.332→29.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.332→1.367 Å / Total num. of bins used: 20
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