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- PDB-3dcm: Crystal structure of the Thermotoga maritima SPOUT family RNA-met... -

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Basic information

Entry
Database: PDB / ID: 3dcm
TitleCrystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine
ComponentsUncharacterized protein TM_1570
KeywordsTRANSFERASE / Trefoil knot / SPOUT Mtase / AdoMet binding
Function / homology
Function and homology information


tRNA (guanine-N(1)-)-methyltransferase, C-terminal / 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 / Uncharacterized protein TM_1570
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKim, D.J. / Kim, H.S. / Lee, S.J. / Suh, S.W.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of Thermotoga maritima SPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine
Authors: Kim, D.J. / Kim, H.S. / Lee, S.J. / Suh, S.W.
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Uncharacterized protein TM_1570
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4072
Polymers22,0081
Non-polymers3981
Water2,306128
1
X: Uncharacterized protein TM_1570
hetero molecules

X: Uncharacterized protein TM_1570
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8134
Polymers44,0172
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3110 Å2
ΔGint-0 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.648, 63.402, 54.522
Angle α, β, γ (deg.)90.000, 129.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-5491-

HOH

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Components

#1: Protein Uncharacterized protein TM_1570 / AdoMet


Mass: 22008.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1570 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9X1Q6
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.43 Å3/Da / Density % sol: 49.37 % / Mosaicity: 0.906 °
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl pH 7.0, 200mM calcium acetate, 20% (v/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 6B11
SYNCHROTRONPAL/PLS 6B21.07163, 1.07204, 1.06261
Detector
TypeIDDetectorDate
Bruker Platinum 1351CCDOct 21, 2004
Bruker Platinum 1352CCDOct 21, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071631
31.072041
41.062611
ReflectionResolution: 2→20 Å / Num. obs: 14038 / % possible obs: 98.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Χ2: 2.005 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.247 / Num. unique all: 1282 / Χ2: 1.432 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→17.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.885 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1412 10.1 %RANDOM
Rwork0.198 ---
obs0.201 14038 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-0.51 Å2
2---1.94 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→17.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 27 128 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221571
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9972125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9675187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46923.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82815287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5181513
X-RAY DIFFRACTIONr_chiral_restr0.3610.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021156
X-RAY DIFFRACTIONr_nbd_refined0.2110.2758
X-RAY DIFFRACTIONr_nbtor_refined0.30.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.221
X-RAY DIFFRACTIONr_mcbond_it0.8581.5965
X-RAY DIFFRACTIONr_mcangle_it1.10721521
X-RAY DIFFRACTIONr_scbond_it1.6083692
X-RAY DIFFRACTIONr_scangle_it2.6144.5604
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 88 -
Rwork0.207 816 -
all-904 -
obs--87.34 %

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