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Yorodumi- PDB-5tk2: Crystal Structure of Uncharacterized Cupredoxin-like domain prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tk2 | ||||||
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Title | Crystal Structure of Uncharacterized Cupredoxin-like domain protein from Bacillus anthracis | ||||||
Components | Cytochrome B | ||||||
Keywords | OXIDOREDUCTASE / Cupredoxin / beta sandwich / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis str. Ames (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Uncharacterized Cupredoxin-like domain protein from Bacillus anthracis Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tk2.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tk2.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 5tk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tk2_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 5tk2_full_validation.pdf.gz | 485.1 KB | Display | |
Data in XML | 5tk2_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 5tk2_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/5tk2 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/5tk2 | HTTPS FTP |
-Related structure data
Related structure data | 4hciS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11088.687 Da / Num. of mol.: 4 / Fragment: UNP residues 33-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria) Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS |
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-Non-polymers , 5 types, 421 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-FMT / | #6: 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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 30.9 % w/v PEG4000, 150 mM Malate pH 5.0, 60 mM Potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2012 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.4→50 Å / Num. obs: 75414 / % possible obs: 94.7 % / Redundancy: 2.9 % / Rsym value: 0.065 / Net I/σ(I): 25.4 | |||||||||||||||
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.6 / % possible all: 61.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HCI Resolution: 1.4→24.25 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.187 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.411 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→24.25 Å
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Refine LS restraints |
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