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Yorodumi- PDB-6b8d: 1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b8d | ||||||
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Title | 1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae | ||||||
Components | Elongation factor GEF-G | ||||||
Keywords | RIBOSOMAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Elongation factor G | ||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / 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: 1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / 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 | 6b8d.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b8d.ent.gz | 135.6 KB | Display | PDB format |
PDBx/mmJSON format | 6b8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/6b8d ftp://data.pdbj.org/pub/pdb/validation_reports/b8/6b8d | HTTPS FTP |
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-Related structure data
Related structure data | 5tv2S 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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Unit cell |
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-Components
#1: Protein | Mass: 45178.871 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-405) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: fusA, fus, HI_0579 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: P43925 |
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#2: Chemical | ChemComp-CL / |
#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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 11.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against screen: Classics II (F6), 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350 |
-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: Aug 8, 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: 1.78→30 Å / Num. obs: 47575 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rsym value: 0.043 / Χ2: 1.011 / Net I/σ(I): 38.4 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2388 / CC1/2: 0.832 / Rpim(I) all: 0.325 / Rsym value: 0.797 / Χ2: 1.003 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TV2 Resolution: 1.78→29.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.841 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.105 / 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: 43.177 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→29.8 Å
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Refine LS restraints |
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