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- PDB-3aia: Crystal structure of DUF358 reveals a putative SPOUT-class methlt... -

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Basic information

Entry
Database: PDB / ID: 3aia
TitleCrystal structure of DUF358 reveals a putative SPOUT-class methltransferase
ComponentsUPF0217 protein MJ1640
KeywordsTRANSFERASE / DUF358 / rRNA methyltransferase / SPOUT-class fold
Function / homology
Function and homology information


tRNA (pseudouridine54-N1)-methyltransferase / tRNA methyltransferase activity / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / cytoplasm
Similarity search - Function
tRNA (pseudouridine(54)-N(1))-methyltransferase, TrmY / Putative SAM-dependent RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
pentane-2,2,4,4-tetrol / S-ADENOSYLMETHIONINE / tRNA (pseudouridine(54)-N(1))-methyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsYuan, Y.A. / Chen, H.Y.
CitationJournal: J Mol Cell Biol / Year: 2010
Title: Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase
Authors: Chen, H.Y. / Yuan, Y.A.
History
DepositionMay 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: 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_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: UPF0217 protein MJ1640
B: UPF0217 protein MJ1640
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6936
Polymers48,6242
Non-polymers1,0694
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-11 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.862, 93.869, 53.837
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0217 protein MJ1640


Mass: 24312.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1640 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59034
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PBL / pentane-2,2,4,4-tetrol


Mass: 136.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PET, MgCl2, Ammonium Fluoride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 77530 / % possible obs: 99.2 % / Redundancy: 7.3 % / Rsym value: 0.045 / Net I/σ(I): 38.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 11.1 / Rsym value: 0.141 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AI9

3ai9


Resolution: 1.4→30.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.121 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21821 4095 5 %RANDOM
Rwork0.18841 ---
obs0.18989 77530 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.783 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å2-1.15 Å2
2---0.59 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 58 490 3798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223372
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9914550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48224.337166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.54215628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8571524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022508
X-RAY DIFFRACTIONr_nbd_refined0.2030.21559
X-RAY DIFFRACTIONr_nbtor_refined0.310.22318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.2106
X-RAY DIFFRACTIONr_mcbond_it0.8551.52044
X-RAY DIFFRACTIONr_mcangle_it1.34823236
X-RAY DIFFRACTIONr_scbond_it2.06731470
X-RAY DIFFRACTIONr_scangle_it3.1574.51314
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 296 -
Rwork0.213 5503 -
obs--95.47 %
Refinement TLS params.Method: refined / Origin x: 11.129 Å / Origin y: 23.2577 Å / Origin z: 13.0305 Å
111213212223313233
T-0.0017 Å20.0099 Å2-0.0016 Å2-0.0104 Å20.0008 Å2--0.0083 Å2
L0.0072 °20.0148 °2-0.018 °2-0.339 °20.0072 °2--0.0511 °2
S-0.0009 Å °0.0002 Å °-0.0066 Å °0.0444 Å °0.0029 Å °-0.0051 Å °-0.0061 Å °-0.0194 Å °-0.002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 199
2X-RAY DIFFRACTION1B1 - 199
3X-RAY DIFFRACTION1A206
4X-RAY DIFFRACTION1B206
5X-RAY DIFFRACTION1A207
6X-RAY DIFFRACTION1B207

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