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Yorodumi- PDB-2a5w: Crystal structure of the oxidized gamma-subunit of the dissimilat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a5w | ||||||
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Title | Crystal structure of the oxidized gamma-subunit of the dissimilatory sulfite reductase (DsrC) from Archaeoglobus fulgidus | ||||||
Components | sulfite reductase, desulfoviridin-type subunit gamma (dsvC) | ||||||
Keywords | OXIDOREDUCTASE / orthogonal helix bundle | ||||||
Function / homology | Function and homology information sulfur carrier activity / tRNA wobble position uridine thiolation / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mander, G.J. / Weiss, M.S. / Hedderich, R. / Kahnt, J. / Ermler, U. / Warkentin, E. | ||||||
Citation | Journal: Febs Lett. / Year: 2005 Title: X-ray structure of the gamma-subunit of a dissimilatory sulfite reductase: Fixed and flexible C-terminal arms. Authors: Mander, G.J. / Weiss, M.S. / Hedderich, R. / Kahnt, J. / Ermler, U. / Warkentin, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5w.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5w.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a5w_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 2a5w_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 2a5w_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2a5w_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5w ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5w | HTTPS FTP |
-Related structure data
Related structure data | 1sauS S: Starting model for refinement |
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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: 13498.659 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: DsrC / Plasmid: pCR2.1-TOPO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28055 #2: Chemical | ChemComp-SO4 / #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: 2.9 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000, Mes/KOH, (NH4)2 SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 24295 / Num. obs: 24295 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.066 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 2005 / Rsym value: 0.38 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAU Resolution: 2.1→28.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.877 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.18 / Stereochemistry target values: Engh & Huber Details: The authors state that the SSBOND between CYS 77 and CYS 85 is partially split, i.e., in only about 50% of all the instances there is a bond and none for the remainder.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.153 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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