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Yorodumi- PDB-1uzr: Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uzr | ||||||
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Title | Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis | ||||||
Components | RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT | ||||||
Keywords | REDUCTASE / RIBONUCLEOTIDE REDUCTASE / TUBERCULOSIS / R2F-2 / RADICAL GENERATION / SMALL SUBUNIT | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Uppsten, M. / Davis, J. / Rubin, H. / Uhlin, U. | ||||||
Citation | Journal: FEBS Lett. / Year: 2004 Title: Crystal Structure of the Biologically Active Form of Class Ib Ribonucleotide Reductase Small Subunit from Mycobacterium Tuberculosis Authors: Uppsten, M. / Davis, J. / Rubin, H. / Uhlin, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uzr.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uzr.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uzr ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uzr | HTTPS FTP |
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-Related structure data
Related structure data | 1r2fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 33842.078 Da / Num. of mol.: 3 / Fragment: RADICAL GENERATING SUBUNIT, RESIDUES 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q50549, UniProt: P9WH71*PLUS, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.3 % |
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Crystal grow | pH: 5.6 / Details: 0.6 M AMSO4, 100MM NACT PH 5.6, 50MM NA/K TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Monochromator: CRYOGENICALLY COOLED HIGH RESOLUTION SI (311) AND LOWER RESOLUTION SI (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 77125 / % possible obs: 99 % / Redundancy: 4.84 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.7 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R2F Resolution: 2.2→111.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.876 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.144 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→111.8 Å
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