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Yorodumi- PDB-6ix6: Crystal structure of the complex of peptidyl-tRNA hydrolase with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ix6 | ||||||
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Title | Crystal structure of the complex of peptidyl-tRNA hydrolase with N-propanol at 1.43 A resolution | ||||||
Components | Peptidyl-tRNA hydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Viswanathan, V. / Sharma, P. / Chaudhary, A. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the complex of peptidyl-tRNA hydrolase with N-propanol at 1.43 A resolution Authors: Viswanathan, V. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ix6.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ix6.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ix6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ix6_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 6ix6_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 6ix6_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 6ix6_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ix6 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ix6 | HTTPS FTP |
-Related structure data
Related structure data | 5y9aS 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: 21222.219 Da / Num. of mol.: 1 / Mutation: R71K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: pth, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase |
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#2: Chemical | ChemComp-POL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 1500, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→38.19 Å / Num. obs: 32796 / % possible obs: 93.7 % / Redundancy: 3.6 % / CC1/2: 0.84 / Rrim(I) all: 0.075 / Net I/σ(I): 9.11 |
Reflection shell | Resolution: 1.43→1.55 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y9A Resolution: 1.43→38.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.022 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.367 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→38.19 Å
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Refine LS restraints |
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