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Yorodumi- PDB-6pe3: Structure of YcaO enzyme from Methanocaldococcus jannaschii in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pe3 | ||||||
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Title | Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with ATP | ||||||
Components | Uncharacterized protein MJ1094 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / YcaO / ATP / thioamide / Methanocaldococcus jannaschii | ||||||
Function / homology | Putative methanogenesis marker protein 1 / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein MJ1094 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dong, S.-H. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2019 Title: Mechanistic Basis for Ribosomal Peptide Backbone Modifications. Authors: Dong, S.H. / Liu, A. / Mahanta, N. / Mitchell, D.A. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pe3.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pe3.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pe3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pe3_validation.pdf.gz | 748.3 KB | Display | wwPDB validaton report |
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Full document | 6pe3_full_validation.pdf.gz | 751.3 KB | Display | |
Data in XML | 6pe3_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 6pe3_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/6pe3 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/6pe3 | HTTPS FTP |
-Related 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: 44228.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1094 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58494 |
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#2: Chemical | ChemComp-ATP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.17 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.6, 2.0 M ammonium sulfate, 0.02 M taurine |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979106 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979106 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25.6 Å / Num. obs: 26776 / % possible obs: 95.61 % / Redundancy: 30.1 % / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Num. unique obs: 1846 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.194 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 68.259 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→25 Å
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Refine LS restraints |
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