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Yorodumi- PDB-4pwa: Crystal structure of the c-type cytochrome SorU from Sinorhizobiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pwa | ||||||
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Title | Crystal structure of the c-type cytochrome SorU from Sinorhizobium meliloti | ||||||
Components | Putative cytochrome C | ||||||
Keywords | ELECTRON TRANSPORT / C-TYPE CYTOCHROME / HEME / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Laming, E.M. / McGrath, A.P. / Maher, M.J. | ||||||
Citation | Journal: Elife / Year: 2015 Title: Structural basis of interprotein electron transfer in bacterial sulfite oxidation. Authors: McGrath, A.P. / Laming, E.L. / Casas Garcia, G.P. / Kvansakul, M. / Guss, J.M. / Trewhella, J. / Calmes, B. / Bernhardt, P.V. / Hanson, G.R. / Kappler, U. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pwa.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pwa.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/4pwa ftp://data.pdbj.org/pub/pdb/validation_reports/pw/4pwa | HTTPS FTP |
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-Related structure data
Related structure data | 4pw3C 4pw9SC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 11403.683 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 28-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02831, SMc04048 / Plasmid: PET-SMC04048TAG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92M25 #2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.8M TRI-SODIUM CITRATE PH 5.5, 0.1M GLYCINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011 |
Radiation | Monochromator: SI VORTEX ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 23434 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4PW9 Resolution: 2.19→39.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.012 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 mean: 32.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→39.19 Å
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Refine LS restraints |
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