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- PDB-3ky7: 2.35 Angstrom resolution crystal structure of a putative tRNA (gu... -

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Basic information

Entry
Database: PDB / ID: 3ky7
Title2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / Putative tRNA (Guanine-7-)-Methyltransferase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Methyltransferase / S-adenosyl-L-methionine / tRNA processing / CSGID
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsHalavaty, A.S. / Minasov, G. / Winsor, J. / Dubrovska, I. / Shuvalova, L. / See, R. / Zoraghi, R. / Reiner, N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252
Authors: Halavaty, A.S. / Minasov, G. / Winsor, J. / Dubrovska, I. / Shuvalova, L. / See, R. / Zoraghi, R. / Reiner, N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)30,8541
Polymers30,8541
Non-polymers00
Water1,49583
1
A: tRNA (guanine-N(1)-)-methyltransferase

A: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)61,7082
Polymers61,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_554-x+3/4,z+1/4,y-1/41
Buried area6370 Å2
ΔGint-27 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.176, 125.176, 125.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase / putative tRNA (guanine-7-)-methyltransferase


Mass: 30853.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: SAR1216, trmD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q6GHJ5, EC: 2.1.1.31
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7.6 mg/mL protein mixed at 1:1 v/v with 1.4 M Na Malonate pH 7.0, 0.1 M Bis-Tris Propane, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 14553 / Num. obs: 14553 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.78
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.5 / Num. unique all: 709 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→27.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.764 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25535 732 5 %RANDOM
Rwork0.20855 ---
obs0.21079 13785 99.83 %-
all-13785 --
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: 24.525 Å2
Refinement stepCycle: LAST / Resolution: 2.35→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 83 1932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221900
X-RAY DIFFRACTIONr_bond_other_d0.0010.021301
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9662571
X-RAY DIFFRACTIONr_angle_other_deg0.92833174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4695228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.85624.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35115338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9091512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_mcbond_it0.7721.51145
X-RAY DIFFRACTIONr_mcbond_other0.2051.5462
X-RAY DIFFRACTIONr_mcangle_it1.38521855
X-RAY DIFFRACTIONr_scbond_it2.3913755
X-RAY DIFFRACTIONr_scangle_it3.9344.5716
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 57 -
Rwork0.263 998 -
obs-998 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.57320.2026-2.08217.6367-4.58566.56880.7399-0.48810.84811.6845-0.48970.0474-0.80330.385-0.25021.3581-0.3426-0.0770.3934-0.02160.21255.153598.570960.1111
26.3961.8164-1.941612.6356-6.47183.8736-0.0746-1.10860.0351.08460.11890.7468-0.54170.1338-0.04421.5481-0.2944-0.10570.8771-0.15060.394658.664798.405163.0614
37.0376-0.14494.15925.6076-3.719816.97950.6375-0.81020.37881.5505-0.506-0.0747-0.8766-0.1343-0.13160.8176-0.23350.11860.1459-0.06260.19657.6905106.862143.8027
41.67631.0939-1.04616.1642-1.20455.8346-0.001-0.2208-0.09830.9436-0.2393-0.3826-0.2520.71920.24020.7394-0.1689-0.09780.4150.11870.270359.316888.796250.5055
51.58611.7248-1.51915.481-3.9592.95890.1097-0.376-0.10770.9447-0.1459-0.0419-0.53720.20890.03620.7781-0.1206-0.0460.29420.04070.146254.842490.205950.3214
61.02130.1297-1.91331.0571-0.55857.48520.23520.01020.04830.145-0.11540.0821-0.6053-0.0723-0.11980.09650.00080.02680.06960.02360.026338.669960.112164.6461
717.3121-7.6484-7.583417.95165.979913.67650.30441.0806-1.8929-0.1466-0.572.20510.3407-1.1780.26560.09150.015-0.06320.3172-0.04880.405232.637850.177955.6193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2A17 - 46
3X-RAY DIFFRACTION3A47 - 76
4X-RAY DIFFRACTION4A77 - 113
5X-RAY DIFFRACTION5A114 - 171
6X-RAY DIFFRACTION6A172 - 231
7X-RAY DIFFRACTION7A232 - 243

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