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- PDB-3ps9: Crystal structure of MnmC from E. coli -

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Basic information

Entry
Database: PDB / ID: 3ps9
TitleCrystal structure of MnmC from E. coli
ComponentstRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC
KeywordsTRANSFERASE / Rossmann Fold / oxidase / methyl transferase / FAD / SAM binding
Function / homology
Function and homology information


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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / S-ADENOSYLMETHIONINE / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsKim, J. / Almo, S.C.
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
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5644
Polymers75,3451
Non-polymers1,2193
Water3,999222
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.063, 100.063, 159.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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


Mass: 75344.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21 / Gene: B21_02209, mnmC, yfcK / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: C5W761, tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M tri-ammonium citrate, PH 7.0, 0.5% ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 27323 / Num. obs: 26488 / % possible obs: 96.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 37.62 Å2 / Rmerge(I) obs: 0.229 / Rsym value: 0.191 / Net I/σ(I): 11.4
Reflection shellResolution: 2.54→2.59 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.1323 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP10.2.23phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.883 / SU B: 19.972 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24661 1328 5 %RANDOM
Rwork0.18179 ---
obs0.18502 25161 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 81 222 5515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215443
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.967423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6324.195267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36415823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2581535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214262
X-RAY DIFFRACTIONr_mcbond_it1.011.53338
X-RAY DIFFRACTIONr_mcangle_it1.91825328
X-RAY DIFFRACTIONr_scbond_it3.17832105
X-RAY DIFFRACTIONr_scangle_it5.0434.52094
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 69 -
Rwork0.221 1436 -
obs--76.36 %
Refinement TLS params.Method: refined / Origin x: -2.3304 Å / Origin y: 34.701 Å / Origin z: -3.0964 Å
111213212223313233
T0.0095 Å2-0.0035 Å20.0014 Å2-0.0229 Å20.0013 Å2--0.0067 Å2
L0.6014 °2-0.0116 °2-0.0285 °2-0.389 °2-0.0701 °2--0.5881 °2
S0.0129 Å °-0.0682 Å °-0.0461 Å °-0.0061 Å °0.0089 Å °0.0095 Å °-0.014 Å °-0.026 Å °-0.0217 Å °

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