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Yorodumi- PDB-3kyw: Xray crystal structure determination of H-labeled perdeuterated r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kyw | ||||||
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Title | Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT / ultra-high resolution room-temperature / Iron / Metal-binding / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Gardberg, A.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. Authors: Gardberg, A.S. / Del Castillo, A.R. / Weiss, K.L. / Meilleur, F. / Blakeley, M.P. / Myles, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kyw.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kyw.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/3kyw ftp://data.pdbj.org/pub/pdb/validation_reports/ky/3kyw | HTTPS FTP |
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-Related structure data
Related structure data | 3kyuC 3kyvC 3kyxC 3kyyC 1brfS C: citing same article (ref.) 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: 6031.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ab-initio perdeuteration / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rub, PF1282 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24297 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Method: hanging drop / Details: 3.8 M sodium/potassium phosphate, hanging drop |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR225 / Detector: CCD / Date: Mar 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→27.4 Å / Num. obs: 21725 / % possible obs: 98.8 % / Redundancy: 3.7 % / Net I/σ(I): 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BRF Resolution: 1.1→26.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.641 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / 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 max: 51.67 Å2 / Biso mean: 15.095 Å2 / Biso min: 7.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→26.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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