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Yorodumi- PDB-3geh: Crystal structure of MnmE from Nostoc in complex with GDP, FOLINI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3geh | ||||||
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Title | Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN | ||||||
Components | tRNA modification GTPase mnmE | ||||||
Keywords | HYDROLASE / G protein / GTPase / tRNA modification / U34 / GTP-binding / Magnesium / Metal-binding / Nucleotide-binding / Potassium / tRNA processing | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / tRNA modification / GTPase activity / GTP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Nostoc sp. PCC (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Meyer, S. / Wittinghofer, A. | ||||||
Citation | Journal: Plos Biol. / Year: 2009 Title: Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy Authors: Meyer, S. / Bohme, S. / Kruger, A. / Steinhoff, H.-J. / Klare, J.P. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3geh.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3geh.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 3geh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3geh ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3geh | HTTPS FTP |
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-Related structure data
Related structure data | 3geeC 3geiC 1xzpS S: Starting model for refinement C: citing same article (ref.) |
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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: 50111.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC (bacteria) / Strain: 7120 / Gene: mnmE, trmE, all4677 / Plasmid: pET14b-NoMnmE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(De3) References: UniProt: Q8YN91, Hydrolases; Acting on acid anhydrides |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-FON / |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.730611 Å3/Da / Density % sol: 81.725288 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM TRIS-HCl, pH 7.5, 22% (w/v) PEG 550 MME, 10mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28186 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 25, 2007 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28186 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. all: 23250 / Num. obs: 23100 / % possible obs: 99.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 76.546 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.178 / Net I/σ(I): 8.61 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 8.03 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.18 / Num. unique all: 2004 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XZP Resolution: 3.2→19.99 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU B: 38.786 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.543 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.281 Å / Total num. of bins used: 20
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