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- PDB-3gee: Crystal structure of MnmE from Chlorobium tepidum in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gee | ||||||
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Title | Crystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID | ||||||
![]() | tRNA modification GTPase mnmE | ||||||
![]() | HYDROLASE / G protein / GTPase / tRNA modification / U34 / Cytoplasm / GTP-binding / Magnesium / Metal-binding / Nucleotide-binding / Potassium / tRNA processing | ||||||
Function / homology | ![]() Hydrolases; Acting on acid anhydrides / tRNA modification / GTPase activity / GTP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meyer, S. / Wittinghofer, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1005.3 KB | Display | ![]() |
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Full document | ![]() | 1014.1 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gehC ![]() 3geiC ![]() 1xzpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52165.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8KAS1, Hydrolases; Acting on acid anhydrides |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-FON / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM TRIS-HCl, pH 8.5, 2.25M NaCl, 15% (w/v) PEG 6000, 5mM GDP, 5mM AlCl3, 50mM NaF, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98003 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→25 Å / Num. all: 18710 / Num. obs: 18513 / % possible obs: 98.9 % / Redundancy: 7.16 % / Biso Wilson estimate: 86.639 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.061 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 7.28 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.4 / Num. unique all: 895 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XZP Resolution: 2.95→19.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / SU B: 37.548 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.353 / 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: 106.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.025 Å / Total num. of bins used: 20
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