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- PDB-3vyw: Crystal structure of MNMC2 from Aquifex Aeolicus -

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Basic information

Entry
Database: PDB / ID: 3vyw
TitleCrystal structure of MNMC2 from Aquifex Aeolicus
ComponentsMNMC2
KeywordsTRANSFERASE / tRNA wobble uridine / modification enzyme / genetic code / 5-methylaminomethyl-2-thiouridine / methyltransferase / 2-codon sets / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1180 / MnmC-like methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase / Vaccinia Virus protein VP39 / Four Helix Bundle (Hemerythrin (Met), subunit A) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / S-ADENOSYLMETHIONINE / MnmC-like methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å
AuthorsShibata, R. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1).
Authors: Kitamura, A. / Nishimoto, M. / Sengoku, T. / Shibata, R. / Jager, G. / Bjork, G.R. / Grosjean, H. / Yokoyama, S. / Bessho, Y.
History
DepositionOct 3, 2012Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 17, 2012ID: 2E58
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MNMC2
B: MNMC2
C: MNMC2
D: MNMC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,58810
Polymers144,7544
Non-polymers1,8346
Water2,630146
1
A: MNMC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5872
Polymers36,1881
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MNMC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7073
Polymers36,1881
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MNMC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7073
Polymers36,1881
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MNMC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5872
Polymers36,1881
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.487, 107.581, 117.711
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.718633, 0.568535, 0.400418), (-0.466047, -0.033597, 0.884122), (0.516107, -0.821973, 0.24082)1.63527, 31.83657, -24.15404
3given(0.996328, 0.027091, 0.081225), (0.084011, -0.12607, -0.988458), (-0.016538, 0.991651, -0.127883)5.18553, -29.32364, -20.05104
4given(0.688412, -0.485075, 0.539251), (-0.50013, -0.855915, -0.131455), (0.525319, -0.179201, -0.831822)-21.76697, 4.1872, -68.57616

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Components

#1: Protein
MNMC2


Mass: 36188.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1980 / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: O67789
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3350, sodium acetate, benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.97923
SYNCHROTRONSPring-8 BL41XU20.97923,0.97952,0.97500
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 12, 2005
ADSC QUANTUM 3152CCDJul 12, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979521
30.9751
ReflectionResolution: 2.49→45.39 Å / Num. obs: 47040 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.6 Å2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 4689 / Rsym value: 0.295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.49→45.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 1.042 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 2272 4.9 %RANDOM
Rwork0.19134 ---
obs0.19453 43644 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.096 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 126 146 10340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.01910421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1232.01414045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47251214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1123.221475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.443151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8891587
X-RAY DIFFRACTIONr_chiral_restr0.1680.21536
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0217701
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.489→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 132 -
Rwork0.299 2788 -
obs--84.2 %

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