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- PDB-3tqs: Structure of the dimethyladenosine transferase (ksgA) from Coxiel... -

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Basic information

Entry
Database: PDB / ID: 3tqs
TitleStructure of the dimethyladenosine transferase (ksgA) from Coxiella burnetii
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / Protein synthesis
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytoplasm
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsRudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references

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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 A
B: Ribosomal RNA small subunit methyltransferase A
C: Ribosomal RNA small subunit methyltransferase A
D: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)118,6544
Polymers118,6544
Non-polymers00
Water19,8891104
1
A: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)29,6631
Polymers29,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)29,6631
Polymers29,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)29,6631
Polymers29,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)29,6631
Polymers29,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.007, 57.895, 112.938
Angle α, β, γ (deg.)90.000, 90.010, 104.340
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ribosomal RNA small subunit methyltransferase A / / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 29663.455 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: rsmA, ksgA, CBU_1982 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83AC2, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1104 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 7.5
Details: 200 mM NaCl, 20% PEG 3350, pH 7.5, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 64960 / Num. obs: 60608 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Χ2: 0.99 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.011.90.06621890.963167.5
2.01-2.051.90.06327690.889186.1
2.05-2.0920.05930230.979192.4
2.09-2.1320.05230390.971193.1
2.13-2.1820.04829790.901193.4
2.18-2.2320.04731080.914193.6
2.23-2.2920.04629670.983193.4
2.29-2.3520.04130750.922194
2.35-2.4220.03930790.871194.4
2.42-2.4920.03930620.974194.9
2.49-2.5820.03830900.942195
2.58-2.6920.03231190.98195.4
2.69-2.8120.03430831.054195.7
2.81-2.9620.03131580.952196
2.96-3.1420.0331070.955196
3.14-3.3920.02531650.995197
3.39-3.7320.02331301.07196.8
3.73-4.2620.02132031.131197.3
4.26-5.3720.02131791.072198.2
5.37-5020.02330841.246195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→17.75 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5533 / SU ML: 0.2 / σ(F): 1.97 / Phase error: 44.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 3048 5.05 %
Rwork0.1835 --
obs0.1866 60349 92.89 %
all-63397 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.176 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 64.98 Å2 / Biso mean: 14.8759 Å2 / Biso min: 2.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.4574 Å2-0.842 Å2-0.5942 Å2
2---1.684 Å2-0.2148 Å2
3---3.1414 Å2
Refinement stepCycle: LAST / Resolution: 1.98→17.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7996 0 0 1104 9100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068184
X-RAY DIFFRACTIONf_angle_d111124
X-RAY DIFFRACTIONf_chiral_restr0.071276
X-RAY DIFFRACTIONf_plane_restr0.0041436
X-RAY DIFFRACTIONf_dihedral_angle_d14.2123060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.04940.27872720.17894595486776
2.0494-2.13140.24522970.17375775607293
2.1314-2.22820.23932990.18415763606293
2.2282-2.34540.25252920.17755784607694
2.3454-2.4920.24433240.17465796612095
2.492-2.68380.26663170.18225863618095
2.6838-2.95280.26432930.18925944623796
2.9528-3.37750.25693250.19375926625196
3.3775-4.24560.23093360.18325968630497
4.2456-17.750.21752930.18595887618095
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)
10.0112-0.01070.00690.0089-0.00680.00360.00560.02990.01520.0001-0.0017-0.0067-0.0099-0.03130.0156-0.07170.0313-0.01640.1020.00720.0218-21.062154.186221.0029
20.00450.00160.00020.00710.00230.00210.03-0.0208-0.01350.026-0.0261-0.008-0.0022-0.00610.0074-0.0123-0.03750.0130.05870.00560.0752-18.674456.517235.0531
30.01970.01440.00180.03340.0026-00.0280.01230.04970.0134-0.0058-0.0182-0.00220.00240.00750.04220.0179-0.0216-0.02730.03160.0681-12.063543.718326.2468
40.0169-0.01370.00450.025-0.0220.0181-0.0181-0.0162-0.00090.00640.0047-0.01750.01590.0193-0.01410.0080.0541-0.0294-0.05220.04340.064-7.312240.298918.9512
50.01670.0177-0.00280.0274-0.00090.002-0.0299-0.02650.00220.04320.004-0.0576-0.0275-0.0102-0.008-0.01280.091-0.0580.0120.07750.03993.725223.50327.4402
60.02430.00950.002300.00060.00190.0354-0.03320.00660.018-0.0067-0.00150.01490.01530.0636-0.1422-0.0751-0.02190.09010.0493-0.026512.672453.696655.0385
70.0207-0.0035-0.00920.01260.00580.00530.01570.0305-0.06410.0284-0.03770.0097-0.0032-0.0161-0.02240.0487-0.1142-0.07970.0811-0.02050.02916.560465.967756.5838
80.00450.00550.00010.00690.000100.01590.00170.0123-0.00080.00350.009-0.008-0.00420.0050.0429-0.036-0.00270.06620.02610.0154-6.224972.153844.2135
90.0395-0.0003-0.0130.01670.00240.0023-0.0250.0163-0.020.00530.03110.03280.0236-0.0480.00330.0428-0.05360.06820.04340.03220.05411.526468.682247.7794
100.0153-0.00540.00430.02460.00870.00410.0046-0.0403-0.00270.00740.00880.0637-0.0033-0.0010.0042-0.09080.0073-0.00920.0578-0.00180.0251-10.861686.296755.6758
110.001-0.00210.00060.0046-0.00170.00120.01170.00130.008-0.02290.0026-0.0167-0.02290.003-0.00010.0876-0.0417-0.009-0.0206-0.00030.0435-21.068554.18177.4705
120.01580.01-0.00830.01430.00060.00810.0083-0.0141-0.00810.01-0.01680.0106-0.0152-0.00450.00310.08710.0283-0.010.0523-0.02740.0266-18.277357.125891.3263
130.085-0.0066-0.0130.0232-0.00240.0205-0.01570.01050.0346-0.0023-0.02770.0130.0306-0.0386-0.02110.038-0.020.01410.1014-0.02940.0174-9.94542.010781.3169
140.0350.01050.00290.01630.00340.0021-0.01530.0404-0.01390.02640.0259-0.00670.00440.0775-0.00030.0676-0.02420.00390.1086-0.00780.004-9.393941.649675.751
150.00780.0068-0.00140.0524-0.02180.029-0.0068-0.02920.0070.0376-0.01-0.0858-0.0030.03930.00070.0717-0.04730.0080.007-0.01670.07673.717323.487183.9181
160.0221-0.00790.0080.00970.00320.0079-0.00790.0336-0.0577-0.012-0.01980.04030.0126-0.001-0.00050.1450.02720.02360.022-0.04690.108212.555554.7437-5.0569
170.0004-0.0001-0.0050.00080.00320.08590.0004-0.02180.04390.0099-0.01230.01060.06230.028-0.00720.05990.06060.0036-0.0015-0.01110.086213.6256.78815.2767
180-0.0033-0.00080.02570.01350.00480.01040.0398-0.0551-0.0048-0.02360.0395-0.0054-0.02670.03260.05250.11460.06710.02920.00210.04832.209466.2436-2.5283
190.0119-0.00360.00440.02770.01670.0115-0.0022-0.00260.00690.01460.0114-0.0024-0.0464-0.01490.00410.060.0391-0.02420.0256-0.0550.06520.160169.5087-9.2814
200.00790.00240.00510.02250.00470.0037-0.0272-0.0044-0.00110.0246-0.01570.05470.0271-0.01430.00030.1623-0.01640.02270.0078-0.05580.1052-10.876186.3173-0.7905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:58)A12 - 58
2X-RAY DIFFRACTION2(chain A and resid 59:96)A59 - 96
3X-RAY DIFFRACTION3(chain A and resid 97:139)A97 - 139
4X-RAY DIFFRACTION4(chain A and resid 140:197)A140 - 197
5X-RAY DIFFRACTION5(chain A and resid 198:258)A198 - 258
6X-RAY DIFFRACTION6(chain B and resid 12:90)B12 - 90
7X-RAY DIFFRACTION7(chain B and resid 91:136)B91 - 136
8X-RAY DIFFRACTION8(chain B and resid 137:149)B137 - 149
9X-RAY DIFFRACTION9(chain B and resid 150:197)B150 - 197
10X-RAY DIFFRACTION10(chain B and resid 198:258)B198 - 258
11X-RAY DIFFRACTION11(chain C and resid 12:58)C12 - 58
12X-RAY DIFFRACTION12(chain C and resid 59:94)C59 - 94
13X-RAY DIFFRACTION13(chain C and resid 95:152)C95 - 152
14X-RAY DIFFRACTION14(chain C and resid 153:197)C153 - 197
15X-RAY DIFFRACTION15(chain C and resid 198:258)C198 - 258
16X-RAY DIFFRACTION16(chain D and resid 12:66)D12 - 66
17X-RAY DIFFRACTION17(chain D and resid 67:106)D67 - 106
18X-RAY DIFFRACTION18(chain D and resid 107:139)D107 - 139
19X-RAY DIFFRACTION19(chain D and resid 140:197)D140 - 197
20X-RAY DIFFRACTION20(chain D and resid 198:258)D198 - 258

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