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Yorodumi- PDB-6l8p: Crystal structure of RidA from Antarctic bacterium Psychrobacter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l8p | ||||||
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Title | Crystal structure of RidA from Antarctic bacterium Psychrobacter sp. PAMC 21119 | ||||||
Components | RidA family protein | ||||||
Keywords | HYDROLASE / RidA / Deamination / Psychrophile / Antarctic bacterium / Cold-adaptability | ||||||
Function / homology | Function and homology information RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Psychrobacter sp. MES7-P7E (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Kwon, S. / Lee, C.W. / Koh, H.Y. / Lee, J.H. / Park, H.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of the reactive intermediate/imine deaminase A homolog from the Antarctic bacterium Psychrobacter sp. PAMC 21119. Authors: Kwon, S. / Lee, C.W. / Koh, H.Y. / Park, H. / Lee, J.H. / Park, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l8p.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l8p.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 6l8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l8p_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6l8p_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6l8p_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6l8p_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l8p ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l8p | HTTPS FTP |
-Related structure data
Related structure data | 3k0tS 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
#1: Protein | Mass: 15665.569 Da / Num. of mol.: 3 / Mutation: D39E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter sp. MES7-P7E (bacteria) / Gene: CXF62_02540 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N5LLK3 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris Propane/HCl (pH 7), 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, and 0.1 M ...Details: 0.1 M Bis-Tris Propane/HCl (pH 7), 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, and 0.1 M ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 24, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 69280 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Χ2: 2.494 / Net I/σ(I): 10.6 / Num. measured all: 479686 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K0T Resolution: 1.601→42.227 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.17 Å2 / Biso mean: 17.355 Å2 / Biso min: 5.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.601→42.227 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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