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- PDB-4bmp: Crystal Structure of Bacillus cereus Ribonucleotide Reductase di-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bmp | ||||||
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Title | Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (2.1 A resolution) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hammerstad, M. / Hersleth, H.-P. / Rohr, A.K. / Andersson, K.K. | ||||||
![]() | ![]() Title: Crystal Structure of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf in Complex with Nrdi. Authors: Hammerstad, M. / Hersleth, H. / Tomter, A.B. / Rohr, A.K. / Andersson, K.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 | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bmoSC ![]() 4bmqC ![]() 4bmrC ![]() 4bmtC ![]() 4bmuC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 37052.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q81G55, ![]() |
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#2: Protein | Mass: 13539.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 121 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | ![]() #5: Chemical | ChemComp-FMN / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow![]() | pH: 7 Details: 10 % (W/V) PEG 8000, 0.2 M MAGNESIUM CHLORIDE AND 0.1 M TRIS, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→62.5 Å / Num. obs: 30834 / % possible obs: 98.5 % / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4BMO Resolution: 2.1→62.59 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.625 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 32.885 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→62.59 Å
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Refine LS restraints |
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