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Yorodumi- PDB-7mmr: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mmr | ||||||
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Title | Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Oxidized Form with Cu(I) bound | ||||||
Components |
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Keywords | OXIDOREDUCTASE/FMN Binding Protein / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / NrdI / FLAVOPROTEIN / OXIDOREDUCTASE-FMN Binding Protein complex | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / membrane Similarity search - Function | ||||||
Biological species | Aerococcus urinae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Palowitch, G.M. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Ribonucleotide Reductase Authors: Palowitch, G.M. / Boal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mmr.cif.gz | 377.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mmr.ent.gz | 306.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/7mmr ftp://data.pdbj.org/pub/pdb/validation_reports/mm/7mmr | HTTPS FTP |
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-Related structure data
Related structure data | 7mmpC 7mmqC 7mmsC 7mmtC 7mmuC 7mmwC 6eboS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ABCDEGFH
#1: Protein | Mass: 38764.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aerococcus urinae (strain ACS-120-V-Col10a) (bacteria) Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: F2I8X9, ribonucleoside-diphosphate reductase #2: Protein | Mass: 15929.860 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aerococcus urinae (bacteria) / Gene: nrdI, CYJ29_07405, DBT54_07500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178HGH7 |
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-Non-polymers , 6 types, 556 molecules
#3: Chemical | ChemComp-CU1 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-FMN / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.52 Å3/Da / Density % sol: 51.27 % / Mosaicity: 0.499 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17% (w/v) PEG 3350, 0.1 M calcium chloride, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 146267 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Χ2: 0.9 / Net I/σ(I): 9.3 / Num. measured all: 1050183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EBO Resolution: 2→34.32 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.382 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.16 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.47 Å2 / Biso mean: 27.852 Å2 / Biso min: 10.44 Å2
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Refinement step | Cycle: final / Resolution: 2→34.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0
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