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Yorodumi- PDB-7ai9: Structure of Ribonucleotide reductase R2 from Escherichia coli co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ai9 | |||||||||
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Title | Structure of Ribonucleotide reductase R2 from Escherichia coli collected by rotation serial crystallography on a COC membrane at a synchrotron source | |||||||||
Components | Ribonucleoside-diphosphate reductase 1 subunit beta | |||||||||
Keywords | OXIDOREDUCTASE / metalloprotein | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Aurelius, O. / John, J. / Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Hogbom, M. / Wang, M. / Marsh, M. | |||||||||
Funding support | Sweden, European Union, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Versatile microporous polymer-based supports for serial macromolecular crystallography. Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ai9.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ai9.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ai9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ai9_validation.pdf.gz | 242.9 KB | Display | wwPDB validaton report |
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Full document | 7ai9_full_validation.pdf.gz | 242.3 KB | Display | |
Data in XML | 7ai9_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 7ai9_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/7ai9 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/7ai9 | HTTPS FTP |
-Related structure data
Related structure data | 7ac2C 7ac3C 7ac4C 7ac5C 7ac6C 7ai8C 1mxrS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43558.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli) References: UniProt: P69924, ribonucleoside-diphosphate reductase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 34-37 % PAA 2100, 100 mM HEPES 7.0, 250-450 mM NaCl, 200 mM ammonium sulfate [and] 26% PAA 2100, 100 mM HEPES 7.0, 150 NaCl, 100 Malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.26 Å / Num. obs: 64377 / % possible obs: 100 % / Redundancy: 26.38 % / Biso Wilson estimate: 59.93 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.197 / Net I/σ(I): 10.05 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 23.1 % / Mean I/σ(I) obs: 0.48 / Num. unique obs: 4762 / CC1/2: 0.183 / Rrim(I) all: 11.05 / % possible all: 99.9 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Sample holding: COC thin membrane |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MXR Resolution: 2→45.26 Å / SU ML: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2222 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.26 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.9362102078 Å / Origin y: 29.8703406673 Å / Origin z: 4.86562357756 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 339) |