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- PDB-3mte: Crystal Structure of 16S rRNA Methyltranferase -

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Basic information

Entry
Database: PDB / ID: 3mte
TitleCrystal Structure of 16S rRNA Methyltranferase
Components16S rRNA methylase
KeywordsTRANSFERASE / Methyltransferase / 16S / Ribosomal / Aminoglycoside / Resistance / RNA
Function / homology
Function and homology information


16S rRNA (adenine1408-N1)-methyltransferase / methyltransferase activity / methylation / response to antibiotic
Similarity search - Function
Putative methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 16S rRNA (adenine(1408)-N(1))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsMacmaster, R.A. / Conn, G.L. / Zelinskaya, N.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structural insights into the function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and human pathogenic bacteria.
Authors: Macmaster, R. / Zelinskaya, N. / Savic, M. / Rankin, C.R. / Conn, G.L.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA methylase
B: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1934
Polymers50,3962
Non-polymers7972
Water4,594255
1
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5962
Polymers25,1981
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5962
Polymers25,1981
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.651, 59.816, 91.697
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 16S rRNA methylase


Mass: 25197.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ARS3 / Gene: npmA / Plasmid: pET44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8C927
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 6000, 4% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2009
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.805→36.3 Å / Num. obs: 49392 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20
Reflection shellResolution: 1.805→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4787 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MQH

3mqh


Resolution: 1.805→36.25 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 1473 3.13 %RANDOM
Rwork0.1728 ---
obs0.1738 47069 95.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.468 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5085 Å20 Å20.6313 Å2
2--4.095 Å20 Å2
3----8.6035 Å2
Refinement stepCycle: LAST / Resolution: 1.805→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 53 255 3830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073774
X-RAY DIFFRACTIONf_angle_d1.0275109
X-RAY DIFFRACTIONf_dihedral_angle_d17.1661416
X-RAY DIFFRACTIONf_chiral_restr0.071563
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.86940.25231280.21393789X-RAY DIFFRACTION80
1.8694-1.94430.24981360.19224281X-RAY DIFFRACTION90
1.9443-2.03270.22721460.17754489X-RAY DIFFRACTION94
2.0327-2.13990.2131420.17544600X-RAY DIFFRACTION96
2.1399-2.27390.2141480.16754640X-RAY DIFFRACTION98
2.2739-2.44950.17891580.16474636X-RAY DIFFRACTION98
2.4495-2.69590.20931540.17964757X-RAY DIFFRACTION99
2.6959-3.08580.241500.18984754X-RAY DIFFRACTION100
3.0858-3.88710.21321560.16914801X-RAY DIFFRACTION100
3.8871-36.25760.16181550.15484849X-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)
11.17230.53740.09580.9677-0.58041.56980.231-0.57340.19070.4567-0.24040.1408-0.0378-0.3023-0.03050.2172-0.10230.04120.3062-0.00640.131926.90916.975243.9988
21.18890.30010.17371.0916-0.34912.56470.0499-0.17730.02420.0923-0.00260.0795-0.0697-0.0645-0.0390.1065-0.03040.01260.1461-0.0150.142729.683819.654628.6045
30.64080.3107-0.26920.6443-0.23981.45930.10240.0110.1929-0.1055-0.10120.2883-0.386-0.1403-0.07630.276-0.02410.02710.1565-0.00150.229532.673935.169217.9062
40.47570.1839-0.03021.1989-0.24451.30020.1093-0.01590.059-0.0392-0.1443-0.1263-0.08660.28810.01790.1187-0.02230.00510.1922-0.00920.170839.146619.842318.8734
50.9022-0.50391.04661.4789-1.29772.4629-0.1945-0.347-0.09640.47620.25080.1804-0.1069-0.236-0.04080.19370.05290.06780.08010.05260.082251.2341-4.837323.3143
60.9363-0.2959-0.09431.6624-1.09482.0734-0.1187-0.055-0.10530.01570.0338-0.04010.2522-0.00270.06980.15440.0190.01230.1203-0.0010.1554.8522-2.596114.6513
71.2015-1.56880.15852.18330.34483.56520.52690.20860.65540.2071-0.2204-0.80360.48920.7653-0.29240.51470.06310.05090.6403-0.16370.561474.99875.9156-1.6049
80.68550.6284-0.08661.31090.5361.27120.01850.12350.074-0.0049-0.02090.01520.01160.01270.01220.12150.0092-0.01520.13290.01980.164458.68729.74567.7967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:155)
3X-RAY DIFFRACTION3(chain A and resid 156:183)
4X-RAY DIFFRACTION4(chain A and resid 184:219)
5X-RAY DIFFRACTION5(chain B and resid 1:60)
6X-RAY DIFFRACTION6(chain B and resid 61:142)
7X-RAY DIFFRACTION7(chain B and resid 143:156)
8X-RAY DIFFRACTION8(chain B and resid 157:219)

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