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Open data
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Basic information
Entry | Database: PDB / ID: 1biq | ||||||
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Title | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN MUTANT E238A | ||||||
![]() | (PROTEIN R2 OF RIBONUCLEOTIDE ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / DNA REPLICATION / IRON | ||||||
Function / homology | ![]() ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Logan, D.T. / Demare, F. / Persson, B.O. / Slaby, A. / Sjoberg, B.M. / Nordlund, P. | ||||||
![]() | ![]() Title: Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins. Authors: Logan, D.T. / deMare, F. / Persson, B.O. / Slaby, A. / Sjoberg, B.M. / Nordlund, P. #1: ![]() Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 Authors: Nordlund, P. / Eklund, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.6 KB | Display | ![]() |
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Full document | ![]() | 478 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xikS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.824671, 0.549974, 0.132088), Vector: |
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Components
-PROTEIN R2 OF RIBONUCLEOTIDE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 43368.828 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Mutation: Y122F, E238A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase |
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#2: Protein | Mass: 43352.828 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Mutation: Y122F, E238A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69924, ribonucleoside-diphosphate reductase |
-Non-polymers , 5 types, 348 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HG.gif)
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#3: Chemical | #4: Chemical | ChemComp-FE / | #5: Chemical | #6: Chemical | ChemComp-HG / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 34 % Description: THE CRYSTAL USED FOR DATA COLLECTION WAS IN THE APO FORM. IT WAS SOAKED WITH FE(II) IONS FOR 3 HOURS BEFORE BEING FLASH-COOLED. DURING THIS TIME THE SIDE CHAIN OF PHE 208 IN MONOMER 1 ...Description: THE CRYSTAL USED FOR DATA COLLECTION WAS IN THE APO FORM. IT WAS SOAKED WITH FE(II) IONS FOR 3 HOURS BEFORE BEING FLASH-COOLED. DURING THIS TIME THE SIDE CHAIN OF PHE 208 IN MONOMER 1 BECAME HYDROXYLATED AT THE EPSILON CARBON THROUGH INTERACTION OF OXYGEN WITH THE DIIRON SITE. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: BENT QUARTZ MIRROR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→27 Å / Num. obs: 161734 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 16.4 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER WITH INITIAL REFINEMENT Starting model: DIFERROUS FORM OF R2 PROTEIN, PDB ENTRY 1XIK Resolution: 2.05→25 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 220 Å2 / ksol: 0.785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→25 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.266 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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