+Open data
-Basic information
Entry | Database: PDB / ID: 5d1p | ||||||
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Title | Archaeal ATP-dependent RNA ligase - form 2 | ||||||
Components | ATP-dependent RNA ligase | ||||||
Keywords | LIGASE / ATP-dependent RNA ligase / Archaea | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å | ||||||
Authors | Murakami, K.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis. Authors: Gu, H. / Yoshinari, S. / Ghosh, R. / Ignatochkina, A.V. / Gollnick, P.D. / Murakami, K.S. / Ho, C.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d1p.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d1p.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d1p_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 5d1p_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 5d1p_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 5d1p_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1p ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1p | 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
#1: Protein | Mass: 43180.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_1221 / Production host: Escherichia coli (E. coli) / References: UniProt: O27289 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M Lithium Sulfate and 40 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5414 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 45957 / % possible obs: 89.3 % / Redundancy: 3.3 % / Net I/σ(I): 9.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→29.365 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.199→29.365 Å
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Refine LS restraints |
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LS refinement shell |
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