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Yorodumi- PDB-8p2d: Cryo-EM structure of the dimeric form of the anaerobic ribonucleo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p2d | |||||||||||||||
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Title | Cryo-EM structure of the dimeric form of the anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP | |||||||||||||||
Components | Anaerobic ribonucleoside-triphosphate reductase | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / ribonucleotide reductase glycyl radical enzyme allosteric regulation nucleotide biosynthesis / OXIDOREDUCTASE | |||||||||||||||
Function / homology | Function and homology information ribonucleoside-triphosphate reductase (thioredoxin) activity / DNA replication / ATP binding Similarity search - Function | |||||||||||||||
Biological species | Segatella copri (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||||||||
Authors | Banerjee, I. / Bimai, O. / Sjoberg, B.M. / Logan, D.T. | |||||||||||||||
Funding support | Sweden, United States, 4items
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Citation | Journal: eLife / Year: 2023 Title: Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site Authors: Bimai, O. / Banerjee, I. / Rozman Grinberg, I. / Huang, P. / Lundin, D. / Sjoberg, B.M. / Logan, D.T. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p2d.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p2d.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 8p2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p2d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8p2d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8p2d_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 8p2d_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/8p2d ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p2d | HTTPS FTP |
-Related structure data
Related structure data | 17361MC 8p23C 8p2cC 8p2sC M: map data used to model this data 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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-Components
#1: Protein | Mass: 84636.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MIQTVVKRDGRIVGFNEQKIMAAIRKAMLHTDKGEDTTLIEQITDHISYRGKSQMSVEAI QDAIEMELMKSARKDVAQKYIAYRNQRNIARKAKTRDVFMSIVNAKNNDITRENANMNAD TPAGMMMKFASETTKPFVDDYLLSEDVRDAVMHNYIHIHDKDYYPTKSLTCVQHPLDVIL ...Details: MIQTVVKRDGRIVGFNEQKIMAAIRKAMLHTDKGEDTTLIEQITDHISYRGKSQMSVEAI QDAIEMELMKSARKDVAQKYIAYRNQRNIARKAKTRDVFMSIVNAKNNDITRENANMNAD TPAGMMMKFASETTKPFVDDYLLSEDVRDAVMHNYIHIHDKDYYPTKSLTCVQHPLDVIL NHGFTAGHGSSRPAKRIETAAVLACISLETCQNEMHGGQAIPAFDFYLAPYVRMSYQEEV KNLEKLTGEDLSNLYDAPIDDYIEKPLDGLQGRERLEQHAINKTVNRVHQAMEAFIHNMN TIHSRGGNQVVFSSINYGTDTSAEGRCIMREILQSTYQGVGNGETAIFPIQIWKKKRGVN YLPEDRNYDLYKLACKVTARRFFPNFLNLDATFNQNEKWRADDPERYKWEIATMGCRTRV FEDRWGEKTSIARGNLSFSTINIVKLAIECMGIENEKQRIDMFFAKLDNILDITAKQLDE RFQFQKTAMAKQFPLLMKYLWVGAENLKPEETIESVINHGTLGIGFIGLAECLVALIGKH HGESEKAQELGLKIITYMRDRANEFSEQYHHNYSILATPAEGLSGKFTKKDRKQFGVIPG VTDRDYYTNSNHVPVYYKCTALKKAQIEAPYHDLTRGGHIFYVEIDGDATHNPSVIESVV DMMDKYNMGYGSVNHNRNRCLDCGYENADAHLEVCPKCGSHHIDKLQRITGYLVGTTDRW NSGKLAELHDRVTHIGGEK Source: (gene. exp.) Segatella copri (bacteria) / Gene: BN510_01369 / Production host: Escherichia coli (E. coli) / References: UniProt: R6BY16 #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.3368 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Prevotella copri (bacteria) | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 1, 5s blot time |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11780 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Details: Patch CTF correction in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5762760 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1132695 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 45 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient Details: Manual fitting was done using Coot and automatic real space refinement used phenix.refine | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8P2C Accession code: 8P2C / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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