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- PDB-3ai9: Crystal structure of DUF358 protein reveals a putative SPOUT-clas... -

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Basic information

Entry
Database: PDB / ID: 3ai9
TitleCrystal structure of DUF358 protein reveals a putative SPOUT-class rRNA methyltransferase
ComponentsUPF0217 protein MJ1640
KeywordsTRANSFERASE / MjDUF358 / 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
S-ADENOSYLMETHIONINE / tRNA (pseudouridine(54)-N(1))-methyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
X: UPF0217 protein MJ1640
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0954
Polymers24,6471
Non-polymers4473
Water3,135174
1
X: UPF0217 protein MJ1640
hetero molecules

X: UPF0217 protein MJ1640
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1898
Polymers49,2952
Non-polymers8946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2940 Å2
ΔGint-17 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.288, 48.133, 62.362
Angle α, β, γ (deg.)90.00, 126.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-449-

HOH

21X-466-

HOH

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Components

#1: Protein UPF0217 protein MJ1640


Mass: 24647.496 Da / Num. of mol.: 1 / Mutation: I190M, I192M, I193M
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.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG, Mg, Tris, Ammonium Fluoride, 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: 0.9797, 0.9799, 0.95
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
30.951
ReflectionResolution: 1.55→50 Å / Num. obs: 25283 / % possible obs: 85.4 % / Redundancy: 3.4 % / Rsym value: 0.038 / Net I/σ(I): 36.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.321 / % possible all: 56.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→34.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.765 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23682 1356 5.1 %RANDOM
Rwork0.18952 ---
obs0.19193 25283 90.49 %-
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: 33.53 Å2
Baniso -1Baniso -2Baniso -3
1-3.49 Å20 Å2-0.37 Å2
2---1.17 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 22 174 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221760
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9832368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49824.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7441513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021313
X-RAY DIFFRACTIONr_nbd_refined0.2170.2791
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.225
X-RAY DIFFRACTIONr_mcbond_it1.1691.51085
X-RAY DIFFRACTIONr_mcangle_it1.64721701
X-RAY DIFFRACTIONr_scbond_it2.8293759
X-RAY DIFFRACTIONr_scangle_it4.2254.5667
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 63 -
Rwork0.308 1187 -
obs--58.3 %
Refinement TLS params.Method: refined / Origin x: 29.2265 Å / Origin y: 44.3873 Å / Origin z: 11.8613 Å
111213212223313233
T-0.1927 Å2-0.0057 Å2-0.0335 Å2--0.064 Å2-0.0134 Å2---0.0739 Å2
L0.4605 °2-0.057 °2-0.5821 °2-2.0025 °20.0667 °2--2.3583 °2
S-0.0314 Å °-0.0125 Å °0.0514 Å °0.0018 Å °0.0613 Å °-0.0456 Å °0.0516 Å °0.0309 Å °-0.0299 Å °

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