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Yorodumi- PDB-6lsp: Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lsp | ||||||
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Title | Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals an inhibited form. | ||||||
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: 1.5 Å | ||||||
Authors | Viswanathan, V. / Ahmad, M.I. / Sharma, P. / Sharma, S. / Singh, T.P. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals on inhibited form. Authors: Viswanathan, V. / Ahmad, M.I. / Sharma, P. / Sharma, S. / 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 | 6lsp.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lsp.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lsp_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 6lsp_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 6lsp_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6lsp_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lsp ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lsp | HTTPS FTP |
-Related structure data
Related structure data | 5yn4S 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: 20967.957 Da / Num. of mol.: 2 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, BIT33_16330, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase #2: 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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 1500, 0.1M HEPES, pH 7.5, 22% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.56 Å / Num. obs: 68761 / % possible obs: 99.97 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4972 / CC1/2: 0.86 / Rpim(I) all: 0.22 / Rrim(I) all: 0.58 / % possible all: 99.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YN4 Resolution: 1.5→33.3 Å / SU ML: 0.1213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9696
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→33.3 Å
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Refine LS restraints |
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LS refinement shell |
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