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- PDB-3geh: Crystal structure of MnmE from Nostoc in complex with GDP, FOLINI... -

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Basic information

Entry
Database: PDB / ID: 3geh
TitleCrystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN
ComponentstRNA modification GTPase mnmE
KeywordsHYDROLASE / 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 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 speciesNostoc sp. PCC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Source and taxonomy / 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)51,1595
Polymers50,1121
Non-polymers1,0474
Water00
1
A: tRNA modification GTPase mnmE
hetero molecules

A: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,31910
Polymers100,2242
Non-polymers2,0958
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9800 Å2
ΔGint-171 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.279, 124.279, 174.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein tRNA modification GTPase mnmE / MnmE


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
#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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 6.730611 Å3/Da / Density % sol: 81.725288 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28186 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 25, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28186 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

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

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
RfactorNum. reflection% reflectionSelection details
Rfree0.26743 1186 5.1 %RANDOM
Rwork0.24053 ---
obs0.24192 21913 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.543 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 64 0 3428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9914727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20325.306147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57415599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0151522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21553
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3881.52256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70423549
X-RAY DIFFRACTIONr_scbond_it0.49331351
X-RAY DIFFRACTIONr_scangle_it0.9194.51178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 71 -
Rwork0.339 1568 -
obs--99.82 %

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