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- PDB-4jwf: Crystal structure of spTrm10(74)-SAH complex -

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Basic information

Entry
Database: PDB / ID: 4jwf
TitleCrystal structure of spTrm10(74)-SAH complex
ComponentstRNA (guanine(9)-N1)-methyltransferase
KeywordsTRANSFERASE / tRNA MTase domain
Function / homology
Function and homology information


tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA N1-guanine methylation / tRNA binding / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha/beta knot - #30 / tRNA (guanine(9)-N(1))-methyltransferase TRM10/TRM10A / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / Alpha/beta knot / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsYan, W. / Shao, Z.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate.
Authors: Shao, Z. / Yan, W. / Peng, J. / Zuo, X. / Zou, Y. / Li, F. / Gong, D. / Ma, R. / Wu, J. / Shi, Y. / Zhang, Z. / Teng, M. / Li, X. / Gong, Q.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine(9)-N1)-methyltransferase
B: tRNA (guanine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9627
Polymers51,0132
Non-polymers9495
Water2,000111
1
A: tRNA (guanine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0114
Polymers25,5071
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA (guanine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9513
Polymers25,5071
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 73.160, 119.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA (guanine(9)-N1)-methyltransferase / tRNA methyltransferase 10 / tRNA(m1G9)-methyltransferase / tRNA(m1G9)MTase


Mass: 25506.688 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 74-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC6B12.09, trm10 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14214, tRNA (guanine9-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 6000, 0.1M Na acetate, pH 5.0, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 27, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→51.89 Å / Num. all: 18531 / Num. obs: 18531 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.6 % / Rsym value: 0.122 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.4-2.5314.20.4491.40.4491100
2.53-2.6814.20.3182.10.3181100
2.68-2.87140.2532.60.2531100
2.87-3.113.90.1723.90.1721100
3.1-3.3913.80.1245.40.1241100
3.39-3.7913.60.16.60.11100
3.79-4.3813.30.0946.80.0941100
4.38-5.3712.10.0956.20.0951100
5.37-7.5912.50.0847.70.0841100
7.59-51.8910.10.06210.40.062197.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.20data reduction
SCALA3.3.20data scaling
SOLVEphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.35 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.077 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26169 940 5.1 %RANDOM
Rwork0.2164 ---
obs0.21883 17384 99.85 %-
all-18351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 64 111 3189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9784206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6724.83147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97915542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.211519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212323
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_it0.6621.51887
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26723040
X-RAY DIFFRACTIONr_scbond_it1.57131217
X-RAY DIFFRACTIONr_scangle_it2.6854.51166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 75 -
Rwork0.248 1265 -
obs--100 %

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