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- PDB-8dq3: X-ray crystal structure of Aggregatibacter actinomycetemcomitans ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dq3 | ||||||
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Title | X-ray crystal structure of Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit | ||||||
![]() | Ribonucleoside-diphosphate reductase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rose, H.R. / Jung, J.J. / Boal, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray crystal structure of Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit Authors: Rose, H.R. / Boal, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268 KB | Display | ![]() |
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PDB format | ![]() | 213 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.3 MB | Display | ![]() |
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Full document | ![]() | 5.3 MB | Display | |
Data in XML | ![]() | 45.2 KB | Display | |
Data in CIF | ![]() | 65.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m8g S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40915.301 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: FXB68_03595 / Production host: ![]() ![]() References: UniProt: A0A142G3G1, ribonucleoside-diphosphate reductase |
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-Non-polymers , 5 types, 603 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.2 M magnesium formate, 16% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→44.22 Å / Num. obs: 148843 / % possible obs: 99.55 % / Redundancy: 7.4 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 27.235 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 14355 / CC1/2: 0.876 / CC star: 0.966 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7M8G ![]() 7m8g Resolution: 1.67→44.22 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.38 Å2 / Biso mean: 15.7885 Å2 / Biso min: 4.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→44.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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