[English] 日本語
![](img/lk-miru.gif)
- PDB-8dq4: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8dq4 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase beta subunit K71R variant | ||||||
![]() | Ribonucleoside-diphosphate reductase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rose, H.R. / Maggiolo, A.O. / Jung, J.J. / Boal, A.K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) class Id ribonucleotide reductase beta subunit K71R variant Authors: Rose, H.R. / Boal, A.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 131 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cwpS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39953.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A5FCJ5, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M magnesium acetate, 20% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 28885 / % possible obs: 98.25 % / Redundancy: 5.8 % / CC1/2: 0.978 / Rpim(I) all: 0.033 / Rrim(I) all: 0.081 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1467 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.097 / Rrim(I) all: 0.239 / % possible all: 98.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6CWP Resolution: 2.35→28.84 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.66 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.67 Å2 / Biso mean: 34.9761 Å2 / Biso min: 5.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→28.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
|