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- PDB-3g88: T. thermophilus 16S rRNA G527 methyltransferase in complex with A... -

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Basic information

Entry
Database: PDB / ID: 3g88
TitleT. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet in space group P61
ComponentsRibosomal RNA small subunit methyltransferase G
KeywordsTRANSFERASE / Methyltransferase / 16S rRNA methyltransferase / translation / Cytoplasm / rRNA processing / S-adenosyl-L-methionine
Function / homology
Function and homology information


16S rRNA (guanine527-N7)-methyltransferase / rRNA (guanine-N7-)-methyltransferase activity / cytosol
Similarity search - Function
rRNA small subunit methyltransferase G / rRNA small subunit methyltransferase G / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase G
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å
AuthorsDemirci, H. / Belardinelli, R. / Gregory, S.T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Rna / Year: 2009
Title: Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG
Authors: Gregory, S.T. / Demirci, H. / Belardinelli, R. / Monshupanee, T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase G
B: Ribosomal RNA small subunit methyltransferase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8857
Polymers53,7692
Non-polymers1,1155
Water12,845713
1
A: Ribosomal RNA small subunit methyltransferase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3893
Polymers26,8851
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal RNA small subunit methyltransferase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4954
Polymers26,8851
Non-polymers6113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.847, 77.847, 167.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase G / 16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited ...16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited division protein B


Mass: 26884.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: gidB, rsmG, TTHA1971 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)Star
References: UniProt: Q9LCY2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 277 K / pH: 8
Details: 20% (w/v) PEG1000, 100 mM imidazole (pH 8.0) and 200 mM calcium acetate, microbatch technique under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.87→25 Å / Num. obs: 47411 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.4 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
RefinementResolution: 1.87→24.38 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.21 / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 2386 5.05 %
Rwork0.17 --
obs0.171 47224 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.97 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 29.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.256 Å20 Å2-0 Å2
2--0.256 Å2-0 Å2
3----0.513 Å2
Refinement stepCycle: LAST / Resolution: 1.87→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 54 734 4454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083831
X-RAY DIFFRACTIONf_angle_d1.4835204
X-RAY DIFFRACTIONf_dihedral_angle_d16.6881493
X-RAY DIFFRACTIONf_chiral_restr0.078597
X-RAY DIFFRACTIONf_plane_restr0.007668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90820.30121500.24492575X-RAY DIFFRACTION98
1.9082-1.94970.19621180.19172630X-RAY DIFFRACTION99
1.9497-1.9950.25411420.18922655X-RAY DIFFRACTION100
1.995-2.04490.22641410.18692631X-RAY DIFFRACTION100
2.0449-2.10020.21441510.16662623X-RAY DIFFRACTION100
2.1002-2.16190.17771510.16772634X-RAY DIFFRACTION100
2.1619-2.23170.19731470.1542610X-RAY DIFFRACTION100
2.2317-2.31140.21441310.16542645X-RAY DIFFRACTION100
2.3114-2.40380.20711300.16152658X-RAY DIFFRACTION100
2.4038-2.51310.20081430.16992657X-RAY DIFFRACTION100
2.5131-2.64550.21011420.16042622X-RAY DIFFRACTION100
2.6455-2.8110.18491520.16792620X-RAY DIFFRACTION100
2.811-3.02770.23651500.17522663X-RAY DIFFRACTION100
3.0277-3.33170.19881500.16932609X-RAY DIFFRACTION100
3.3317-3.81220.1721450.152651X-RAY DIFFRACTION100
3.8122-4.79690.15211200.1392685X-RAY DIFFRACTION100
4.7969-24.38210.19941230.17812670X-RAY DIFFRACTION99
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)
10.7045-0.33320.27031.9165-0.50840.68360.0197-0.0459-0.07670.0790.003-0.22040.0369-0.0376-0.03770.16870.0007-0.03990.1551-0.00910.1816-9.998731.66513.5554
20.2212-0.13710.31880.9893-0.18760.392-0.0757-0.04430.12540.1718-0.0313-0.305-0.06720.06840.06760.1546-0.016-0.03540.1549-0.02420.1816-10.216147.17513.9323
32.4183-1.094-0.32430.6174-0.87811.4553-0.4134-0.11570.57380.32870.2998-0.1597-0.25910.11010.03330.2334-0.0314-0.04670.1576-0.02820.2157-15.58255.741118.2516
40.9065-0.63910.71370.62090.10910.50640.0225-0.00750.1671-0.1446-0.06340.0226-0.0677-0.10360.03790.1803-0.015-0.01740.1637-0.01690.1753-24.223851.4767.2553
52.07540.56380.35520.9206-0.2990.68290.03540.05040.1088-0.1029-0.08750.1404-0.0571-0.10440.04390.1833-0.0002-0.05130.1502-0.00220.1399-29.716848.58614.8055
61.0534-0.63150.30110.9541-0.69030.77740.02210.08080.2134-0.0399-0.0142-0.04810.0112-0.0348-0.01620.17260.00420.03120.16520.02510.1854-16.640543.0084-20.768
70.5159-0.1473-0.08790.5966-0.07990.01080.029-0.02390.1867-0.07650.0123-0.2865-0.07050.0524-0.03450.1409-0.00550.0070.1638-0.01330.1783-5.593333.7803-16.3659
80.8136-0.1965-0.23120.7324-0.26890.30680.06270.1330.1599-0.0861-0.1221-0.32470.00130.25860.06680.1467-0.00890.04420.19210.03020.1765-1.12434.7246-23.8766
90.97030.72940.44250.35890.7380.7072-0.01580.0969-0.16040.0134-0.0465-0.01080.2443-0.03330.0760.18730.01350.03420.19380.00720.27091.587717.0478-21.1692
101.8710.0286-0.23052.1001-0.45741.0321-0.0699-0.0495-0.16930.05630.03730.01520.1172-0.00470.03640.1393-0.00140.02030.15650.02840.1316-9.971519.0858-12.6449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 4:79
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 80:132
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 133:138
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 139:190
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 191:249
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 4:78
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 79:101
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 102:137
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 138:144
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 145:249

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