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- PDB-3sgl: The crystal structure of MnmC from Yersinia pestis bound with FAD... -

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Basic information

Entry
Database: PDB / ID: 3sgl
TitleThe crystal structure of MnmC from Yersinia pestis bound with FAD and SAM
ComponentstRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC
Keywordstransferase / oxidoreductase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Rossmann Fold / methyltransferase / FAD binding SAM binding / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors / tRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity / oxidoreductase activity, acting on the CH-NH group of donors / tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / tRNA wobble uridine modification / tRNA methylation / flavin adenine dinucleotide binding / oxidoreductase activity / cytoplasm
Similarity search - Function
: / tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal / tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / MnmC-like methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain ...: / tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal / tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / MnmC-like methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Vaccinia Virus protein VP39 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / S-ADENOSYLMETHIONINE / tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKim, J. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.
Authors: Kim, J. / Almo, S.C.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Structure summary
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5844
Polymers77,3641
Non-polymers1,2193
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.085, 59.815, 100.797
Angle α, β, γ (deg.)90.00, 100.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC / tRNA mnm(5)s(2)U biosynthesis bifunctional protein / tRNA (mnm(5)s(2)U34)-methyltransferase / FAD- ...tRNA mnm(5)s(2)U biosynthesis bifunctional protein / tRNA (mnm(5)s(2)U34)-methyltransferase / FAD-dependent cmnm(5)s(2)U34 oxidoreductase


Mass: 77364.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mnmC, YPO2756, y1590, YP_2407 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q8ZD36, tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase, Oxidoreductases; Acting on the CH-NH group of donors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES PH 7.0 30% (v/v) Jeffamine ED-2001 PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 21571 / Num. obs: 21571 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.143 / Rsym value: 0.177 / Net I/σ(I): 9.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.819 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3PVC

3pvc


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.848 / SU B: 12.081 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25933 1022 5.1 %RANDOM
Rwork0.1801 ---
obs0.18413 18983 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.3 Å2
2--0.51 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 81 91 5088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9557004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3723.525244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60715771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1831537
X-RAY DIFFRACTIONr_chiral_restr0.0930.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213994
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8681.53140
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71225011
X-RAY DIFFRACTIONr_scbond_it2.94231995
X-RAY DIFFRACTIONr_scangle_it4.7744.51993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 31 -
Rwork0.195 686 -
obs--46.05 %

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