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- PDB-3gee: Crystal structure of MnmE from Chlorobium tepidum in complex with... -

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Basic information

Entry
Database: PDB / ID: 3gee
TitleCrystal structure of MnmE from Chlorobium tepidum in complex with GDP and FOLINIC ACID
ComponentstRNA modification GTPase mnmE
KeywordsHYDROLASE / G protein / GTPase / tRNA modification / U34 / Cytoplasm / GTP-binding / Magnesium / Metal-binding / Nucleotide-binding / Potassium / tRNA processing
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / GTPase activity / GTP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
tRNA modification GTPase MnmE domain 2 / tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / Probable tRNA modification gtpase trme; domain 1 ...tRNA modification GTPase MnmE domain 2 / tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / Probable tRNA modification gtpase trme; domain 1 / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / Gyrase A; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FON / GUANOSINE-5'-DIPHOSPHATE / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.95 Å
AuthorsMeyer, S. / Wittinghofer, A.
CitationJournal: 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
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0823
Polymers52,1651
Non-polymers9172
Water00
1
A: tRNA modification GTPase mnmE
hetero molecules

A: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1646
Polymers104,3312
Non-polymers1,8334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area7530 Å2
ΔGint-33 kcal/mol
Surface area40140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.804, 130.804, 200.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein tRNA modification GTPase mnmE / MnmE


Mass: 52165.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (bacteria) / Gene: mnmE, CT2084, thdF, trmE / Plasmid: pET14b-CtMnmE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3)
References: UniProt: Q8KAS1, Hydrolases; Acting on acid anhydrides
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.08 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98003 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98003 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1XZP

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
RfactorNum. reflection% reflectionSelection details
Rfree0.26951 941 5.1 %RANDOM
Rwork0.23203 ---
obs0.23383 17528 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 62 0 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9994548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3775424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0923.919148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40315587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9841529
X-RAY DIFFRACTIONr_chiral_restr0.0740.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022491
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22322
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3161.52174
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56923374
X-RAY DIFFRACTIONr_scbond_it0.52331311
X-RAY DIFFRACTIONr_scangle_it0.9044.51174
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 66 -
Rwork0.373 1261 -
obs--99.7 %

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