[English] 日本語
Yorodumi- PDB-5ome: The cryofrozen atomic resolution X-ray crystal structure of the r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ome | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution) | |||||||||||||||
Components | Rubredoxin | |||||||||||||||
Keywords | ELECTRON TRANSPORT / Perdeuterated rubredoxin / pyrococcus furiosus / atomic resolution / cryofrozen / reduced / iron | |||||||||||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | |||||||||||||||
Biological species | Pyrococcus furiosus (archaea) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.747 Å | |||||||||||||||
Authors | Cuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T. | |||||||||||||||
Funding support | United Kingdom, France, 4items
| |||||||||||||||
Citation | Journal: To Be Published Title: The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution) Authors: Cuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ome.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ome.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ome.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ome_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ome_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 5ome_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5ome_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5ome ftp://data.pdbj.org/pub/pdb/validation_reports/om/5ome | HTTPS FTP |
-Related structure data
Related structure data | 5nvt |
---|---|
Similar 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: perdeuterated form Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Gene: rub, PF1282 / Plasmid: PET28 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P24297 | ||
---|---|---|---|
#2: Chemical | ChemComp-FE / | ||
#3: Chemical | ChemComp-NA / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % Description: bipyramid bright red (Fe3+), Subsequently reduced with Na2S2O3 to get transparent (Fe2+) crystal. X-ray data collection performed with helicoidal strategy over 180 degrees rotation. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: SEEDED 3.4M EQUIMOLAR NA/K PHOSPHATE BUFFER / Temp details: controlled room |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Cryostream frozen (never flash frozen in liquid N2) |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.77 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Resolution: 0.747→34.8 Å / Num. obs: 57618 / % possible obs: 85.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 4.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.06 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 0.75→0.79 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2727 / CC1/2: 0.786 / Rpim(I) all: 0.17 / Rrim(I) all: 0.266 / % possible all: 28.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.747→18.363 Å / SU ML: 0.02 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.12 Details: Deuterium atoms are isotropic, protein atoms, Fe atom and solvent O atoms are anisotropic
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.747→18.363 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|