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Yorodumi- PDB-1st9: Crystal Structure of a Soluble Domain of ResA in the Oxidised Form -
+Open data
-Basic information
Entry | Database: PDB / ID: 1st9 | ||||||
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Title | Crystal Structure of a Soluble Domain of ResA in the Oxidised Form | ||||||
Components | Thiol-disulfide oxidoreductase resA | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin-like Domain / Alpha-Beta Protein / Soluble Domain / Membrane Protein | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Crow, A. / Acheson, R.M. / Le Brun, N.E. / Oubrie, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Basis of Redox-coupled Protein Substrate Selection by the Cytochrome c Biosynthesis Protein ResA. Authors: Crow, A. / Acheson, R.M. / Le Brun, N.E. / Oubrie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1st9.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1st9.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 1st9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1st9_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 1st9_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 1st9_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1st9_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/1st9 ftp://data.pdbj.org/pub/pdb/validation_reports/st/1st9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | Biological Unit is a Monomer of ResA |
-Components
#1: Protein | Mass: 15942.131 Da / Num. of mol.: 2 / Fragment: Soluble Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: RESA, BSU23150 / Plasmid: pRAN8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35160 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 24-27% PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 4.8 - 5.8, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.4→50 Å / Num. all: 68355 / Num. obs: 67398 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rsym value: 0.052 / Net I/σ(I): 26 | |||||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.1 % / Num. unique all: 5905 / Rsym value: 0.446 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Se-Met Protein Model obtained by MAD methods Resolution: 1.5→28.63 Å / Cor.coef. Fo:Fc: 0.977 / SU B: 0.485 / SU ML: 0.019 / Isotropic thermal model: Individual Atomic Anisotropic B / σ(F): 1 / σ(I): 1 / ESU R: 0.053 / Stereochemistry target values: maximum likelihood Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5% of the data was used as 'Rfree' throughout refinement to give Rfree=15, Rwork=12.3. Subsequently, a final round of refinement using all ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5% of the data was used as 'Rfree' throughout refinement to give Rfree=15, Rwork=12.3. Subsequently, a final round of refinement using all available data, including reflections marked as Rfree in the sf file, was performed to give a final crystallographic Rfactor (Rcryst=12.3).
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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: 12.836 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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