[English] 日本語
Yorodumi- PDB-3rzt: Neutron structure of perdeuterated rubredoxin using rapid (14 hou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rzt | ||||||
---|---|---|---|---|---|---|---|
Title | Neutron structure of perdeuterated rubredoxin using rapid (14 hours) data | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT / Iron / metal-binding / transport | ||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.7504 Å | ||||||
Authors | Munshi, P. / Chung, C.-L. / Weiss, K.L. / Blakeley, M.P. / Myles, D.A.A. / Meilleur, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Authors: Munshi, P. / Chung, S.L. / Blakeley, M.P. / Weiss, K.L. / Myles, D.A. / Meilleur, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3rzt.cif.gz | 31.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3rzt.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rzt_validation.pdf.gz | 319.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3rzt_full_validation.pdf.gz | 319.1 KB | Display | |
Data in XML | 3rzt_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 3rzt_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/3rzt ftp://data.pdbj.org/pub/pdb/validation_reports/rz/3rzt | HTTPS FTP |
-Related structure data
Related structure data | 3rygC 3rz6C 3ss2C 3kywS 3rzr C: citing same article (ref.) S: Starting model for refinement |
---|---|
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 Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1282, rub / 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: NEUTRON DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mg/ml rubredoxin in 1.9 M sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
---|
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: NUCLEAR REACTOR / Site: ILL / Beamline: LADI III / Wavelength: 3.2 - 4.2 | |||||||||
Detector | Type: MAATEL QLD: LADI-III / Detector: IMAGE PLATE / Date: Jun 8, 2007 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.75→27.21 Å / Num. all: 4188 / Num. obs: 4187 / % possible obs: 77.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.4 | |||||||||
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.6 / % possible all: 56.2 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3KYW Resolution: 1.7504→27.208 Å / SU ML: 0.44 / σ(F): 1.53 / Phase error: 21.95 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.505 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7504→27.208 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7504→27.2108 Å
|