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- PDB-3gei: Crystal structure of MnmE from Chlorobium tepidum in complex with GCP -

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Basic information

Entry
Database: PDB / ID: 3gei
TitleCrystal structure of MnmE from Chlorobium tepidum in complex with GCP
ComponentstRNA modification GTPase mnmE
KeywordsHYDROLASE / G protein / G domain / GTPase / GidA / tRNA modification / U34 / GTP-binding / THF-binding / Cytoplasm / 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: tRNA modification GTPase mnmE
B: tRNA modification GTPase mnmE
C: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5636
Polymers156,4963
Non-polymers1,0673
Water00
1
A: tRNA modification GTPase mnmE
hetero molecules

A: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4226
Polymers104,3312
Non-polymers1,0914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5720 Å2
ΔGint-53 kcal/mol
Surface area41090 Å2
MethodPISA
2
B: tRNA modification GTPase mnmE
C: tRNA modification GTPase mnmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8523
Polymers104,3312
Non-polymers5211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-29 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.882, 224.572, 156.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
13B
23C

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLYGLYAA9 - 23012 - 233
211PROPROGLYGLYBB9 - 23012 - 233
311PROPROGLYGLYCC9 - 23012 - 233
121SERSERLYSLYSAA403 - 473406 - 476
221SERSERLYSLYSBB403 - 473406 - 476
321SERSERLYSLYSCC403 - 473406 - 476
112VALVALASPASPAA231 - 391234 - 394
212VALVALASPASPBB231 - 391234 - 394
113SERSERLEULEUBB4 - 87 - 11
213SERSERLEULEUCC4 - 87 - 11

NCS ensembles :
ID
1
2
3

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Components

#1: Protein tRNA modification GTPase mnmE / MnmE


Mass: 52165.285 Da / Num. of mol.: 3
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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, 46mM NaOH, 12% PEG 4000, 40mM NaCl, 5mM GCP, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2006 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 34300 / Num. obs: 34042 / % possible obs: 99.2 % / Redundancy: 7.45 % / Biso Wilson estimate: 92.53 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.131 / Net I/σ(I): 12.13
Reflection shellResolution: 3.4→3.425 Å / Redundancy: 7.61 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.02 / Num. unique all: 719 / % possible all: 100

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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: 3.4→19.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.912 / SU B: 61.478 / SU ML: 0.438 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26891 1721 5.1 %RANDOM
Rwork0.245 ---
obs0.24624 32320 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.559 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2---5.79 Å20 Å2
3---6.6 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8715 0 65 0 8780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228888
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.98412022
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60751140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35123.463387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.652151536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4031582
X-RAY DIFFRACTIONr_chiral_restr0.0810.21424
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.24028
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26122
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5371.55848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00529038
X-RAY DIFFRACTIONr_scbond_it1.14433349
X-RAY DIFFRACTIONr_scangle_it2.1064.52984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2224tight positional0.020.05
12B2224tight positional0.020.05
13C2224tight positional0.020.05
21A924tight positional0.020.05
31B40tight positional0.020.05
11A2224tight thermal0.040.5
12B2224tight thermal0.030.5
13C2224tight thermal0.030.5
21A924tight thermal0.030.5
31B40tight thermal0.030.5
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 115 -
Rwork0.357 2377 -
obs--100 %

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