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Yorodumi- PDB-7qcf: X-ray crystallographic structure of E. coli K-12 glycyl-tRNA synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qcf | ||||||
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Title | X-ray crystallographic structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit (glyQ) | ||||||
Components | Glycine--tRNA ligase alpha subunit | ||||||
Keywords | LIGASE / tRNA glycine | ||||||
Function / homology | Function and homology information glycine-tRNA ligase complex / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Weeks, S.D. / Munawar, A.H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit (glyQ) Authors: Weeks, S.D. / Munawar, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qcf.cif.gz | 231.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qcf.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 7qcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qcf_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 7qcf_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 7qcf_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 7qcf_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qcf ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qcf | HTTPS FTP |
-Related structure data
Related structure data | 5f5wS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34876.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: glyQ, glyS(A), b3560, JW3531 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00960, glycine-tRNA ligase |
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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: 5.98 Å3/Da / Density % sol: 79.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Morpheus buffer system 1, 0.5-3% w/v PEG 8000 and 20 % w/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9775 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3→49.43 Å / Num. obs: 68043 / % possible obs: 100 % / Redundancy: 26.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.057 / Rrim(I) all: 0.296 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F5W Resolution: 3→49.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.573 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.19 Å2 / Biso mean: 89.276 Å2 / Biso min: 29.79 Å2
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Refinement step | Cycle: final / Resolution: 3→49.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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