[English] 日本語
Yorodumi- PDB-6jkx: Crystal structure of peptidyl-tRNA hydrolase with multiple sodium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jkx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of peptidyl-tRNA hydrolase with multiple sodium and chloride ions at 1.08 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: 1.08 Å | ||||||
Authors | Viswanathan, V. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of peptidyl-tRNA hydrolase with multiple sodium and chloride ions at 1.08 A resolution. Authors: Viswanathan, V. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jkx.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jkx.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jkx_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jkx_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 6jkx_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 6jkx_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jkx ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jkx | HTTPS FTP |
-Related structure data
Related structure data | 5y9aS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21250.232 Da / Num. of mol.: 1 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 BL21 (bacteria) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MOH / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.45 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97199 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→50.03 Å / Num. obs: 71837 / % possible obs: 98.59 % / Redundancy: 7.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.057 / Rrim(I) all: 0.178 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.08→1.16 Å / Rmerge(I) obs: 1.497 / Num. unique obs: 2990 / CC1/2: 0.565 / Rpim(I) all: 0.517 / Rrim(I) all: 1.588 / % possible all: 67.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y9A Resolution: 1.08→50.03 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.298 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.944 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.08→50.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|