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- PDB-3g05: Crystal structure of N-terminal domain (2-550) of E.coli MnmG -

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Basic information

Entry
Database: PDB / ID: 3g05
TitleCrystal structure of N-terminal domain (2-550) of E.coli MnmG
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
KeywordsRNA BINDING PROTEIN / tRNA-modification enzyme / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / FAD / Flavoprotein / NAD / tRNA processing
Function / homology
Function and homology information


tRNA wobble uridine modification / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / Glucose inhibited division protein A family signature 1. / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A ...Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / Glucose inhibited division protein A family signature 1. / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesEscherichia coli O157:H7 EDL933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.49 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2009
Title: Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme.
Authors: Shi, R. / Villarroya, M. / Ruiz-Partida, R. / Li, Y. / Proteau, A. / Prado, S. / Moukadiri, I. / Benitez-Paez, A. / Lomas, R. / Wagner, J. / Matte, A. / Velazquez-Campoy, A. / Armengod, M.E. / Cygler, M.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
B: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2836
Polymers127,8982
Non-polymers3844
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-7.3 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.593, 144.593, 271.019
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG / Glucose-inhibited division protein A


Mass: 63949.191 Da / Num. of mol.: 2 / Fragment: N-terminal domain: UNP residues 2-550
Source method: isolated from a genetically manipulated source
Details: N-terminal 2-550 construct with residues 551-629 truncated
Source: (gene. exp.) Escherichia coli O157:H7 EDL933 (bacteria)
Strain: O157:H7 EDL933 / EHEC / Gene: ECs4683, gidA, mnmG, Z5241 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XAY0
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 6.39 Å3/Da / Density % sol: 80.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.3M Lithium sulfate, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 42430 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.108 / Χ2: 0.999 / Net I/σ(I): 16.462
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.49-3.616.10.6441500.991198.5
3.61-3.767.10.44341351.002199.9
3.76-3.937.40.32842131.0031100
3.93-4.147.50.24241940.9991100
4.14-4.47.50.16442141.0021100
4.4-4.747.50.12142160.9981100
4.74-5.217.80.102424011100
5.21-5.978.20.097425711100
5.97-7.5190.06243070.9971100
7.51-509.80.03145040.998199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.66 Å49.74 Å
Translation3.66 Å49.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CES

3ces


Resolution: 3.49→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.827 / SU B: 40.302 / SU ML: 0.29 / SU R Cruickshank DPI: 0.837 / SU Rfree: 0.424 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.837 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2137 5 %RANDOM
Rwork0.227 ---
obs0.229 42341 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.12 Å2 / Biso mean: 83.324 Å2 / Biso min: 37.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 3.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8136 0 20 0 8156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228294
X-RAY DIFFRACTIONr_angle_refined_deg2.3331.96811229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.77551043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61323.894398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.702151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5421577
X-RAY DIFFRACTIONr_chiral_restr0.1730.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216342
X-RAY DIFFRACTIONr_mcbond_it0.761.55220
X-RAY DIFFRACTIONr_mcangle_it1.228370
X-RAY DIFFRACTIONr_scbond_it0.96433074
X-RAY DIFFRACTIONr_scangle_it1.7784.52859
LS refinement shellResolution: 3.49→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 151 -
Rwork0.297 2898 -
all-3049 -
obs--97.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0757-0.34470.16441.0035-0.13490.78890.00830.2489-0.05520.0322-0.15440.0233-0.0030.01020.1461-0.04210.22430.0659-0.066-0.0005-0.210133.458559.603121.7669
20.9772-0.4629-0.35431.22190.20531.1941-0.0120.00150.05870.29310.02270.07840.0178-0.0768-0.01070.09620.22680.0809-0.18330.0025-0.21213.669387.925647.7793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 550
2X-RAY DIFFRACTION2B2 - 550

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