[English] 日本語
Yorodumi- PDB-3kyv: Denovo X-ray crystal structure determination of H-labeled perdeut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kyv | ||||||
---|---|---|---|---|---|---|---|
Title | Denovo X-ray crystal structure determination of H-labeled perdeuterated rubredoxin at 100K | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT / selective perdeuteration / Iron / Metal-binding / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kyv.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kyv.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/3kyv ftp://data.pdbj.org/pub/pdb/validation_reports/ky/3kyv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.71 % |
---|---|
Crystal grow | Method: hanging drop / Details: 3.8 M sodium/potassium phosphate, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR / 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→43.073 Å / Num. obs: 20908 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.1→27.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.501 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 42.34 Å2 / Biso mean: 8.84 Å2 / Biso min: 3.43 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→27.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
|