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Yorodumi- PDB-6bk7: 1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bk7 | ||||||
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Title | 1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis | ||||||
Components | Elongation factor G | ||||||
Keywords | RIBOSOMAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation factor G | ||||||
Function / homology | Function and homology information translation elongation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bk7.cif.gz | 327.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bk7.ent.gz | 267.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bk7_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 6bk7_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 6bk7_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 6bk7_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bk7 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bk7 | HTTPS FTP |
-Related structure data
Related structure data | 5vh6S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45440.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Strain: ATCC 700802 / V583 / Gene: fusA, EF_0200 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q839G9 #2: Chemical | #3: 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: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 12.5 mg/mL protein in 0.5 sodium chloride, 0.01 M Tris, pH 8.3 against screen PEGs II (G6), 15% w/v PEG6000, 5% w/v glycerol, cryoprotectant: reservoir |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2017 / Details: C(111) |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. obs: 69321 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.025 / Rrim(I) all: 0.052 / Rsym value: 0.046 / Χ2: 1.004 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3419 / CC1/2: 0.774 / Rpim(I) all: 0.423 / Rrim(I) all: 0.9 / Rsym value: 0.793 / Χ2: 1.006 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5VH6 Resolution: 1.83→28.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.395 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.127 / 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: 48.832 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→28.95 Å
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Refine LS restraints |
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