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- PDB-3mq2: Crystal Structure of 16S rRNA Methyltranferase KamB -

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Basic information

Entry
Database: PDB / ID: 3mq2
TitleCrystal Structure of 16S rRNA Methyltranferase KamB
Components16S rRNA methyltransferase
KeywordsTRANSFERASE / Methyltranferase / Ribosomal / 16S / Antibiotic Resistance / Aminoglycoside / S-Adenosyl-L-Methionine
Function / homologyVaccinia Virus protein VP39 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesStreptomyces sp. DSM 40477 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsMacmaster, R.A.
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 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,7124
Polymers47,9432
Non-polymers7692
Water5,224290
1
A: 16S rRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers23,9711
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers23,9711
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.302, 64.112, 72.069
Angle α, β, γ (deg.)90.00, 104.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 16S rRNA methyltransferase


Mass: 23971.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. DSM 40477 (bacteria) / Gene: kamb / Plasmid: pET44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAS PER THE AUTHORS THE SEQUENCE DEPOSITED IN THIS ENTRY IS THE FULL LENGTH PROTEIN LISTED IN UNP ...AS PER THE AUTHORS THE SEQUENCE DEPOSITED IN THIS ENTRY IS THE FULL LENGTH PROTEIN LISTED IN UNP ENTRY Q2MFK4. HOWEVER, Q2MFK4 HAS NOT BEEN UPDATED WITH THE FULL SEQUENCE OF THIS PROTEIN AT THE TIME OF PROCESSING THE PDB ENTRY 3MQ2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.25M Potassium thiocyanate, 24% PEG 2000 monomethylether, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 10, 2009
MARMOSAIC 225 mm CCD2CCDJun 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 46638 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.4 / % possible all: 92

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Processing

Software
NameClassification
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.69→25.081 Å / SU ML: 0.18 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2338 5.01 %
Rwork0.1739 --
obs0.1757 46637 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.737 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso mean: 19.89 Å2
Refinement stepCycle: LAST / Resolution: 1.69→25.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 52 290 3674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063585
X-RAY DIFFRACTIONf_angle_d1.1064896
X-RAY DIFFRACTIONf_dihedral_angle_d10.6751376
X-RAY DIFFRACTIONf_chiral_restr0.079528
X-RAY DIFFRACTIONf_plane_restr0.005640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.75060.22582000.17294067X-RAY DIFFRACTION90
1.7506-1.82060.21252320.16614246X-RAY DIFFRACTION95
1.8206-1.90350.21872030.15984406X-RAY DIFFRACTION97
1.9035-2.00380.22312470.15344422X-RAY DIFFRACTION98
2.0038-2.12930.18082230.15314465X-RAY DIFFRACTION99
2.1293-2.29360.19252600.15554510X-RAY DIFFRACTION99
2.2936-2.52420.20862410.16464474X-RAY DIFFRACTION100
2.5242-2.8890.21772270.184549X-RAY DIFFRACTION100
2.889-3.6380.2072440.1854555X-RAY DIFFRACTION100
3.638-25.08420.20912610.18374605X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.679-0.26070.15971.13910.15490.8517-0.10090.05360.00570.02320.0632-0.13940.02020.1059-0.02520.0547-0.01280.00210.0853-0.00690.0709-2.9405-8.164225.8202
20.24280.25590.22730.90750.40680.9867-0.0424-0.02440.0187-0.1045-0.01970.026-0.09220.03370.03140.0730.00760.00760.05030.00610.0497
30.52960.27030.2360.8810.50040.8541-0.07310.10330.0171-0.34880.06990.0442-0.1830.01030.05250.15340.0162-0.03340.07450.00620.048
40.7589-0.23230.15740.9359-0.02470.7556-0.0287-0.0673-0.05740.04020.0390.153-0.0634-0.07320.00930.0397-0.00690.00290.08060.00930.0872
50.38370.2989-0.07720.70080.00080.5656-0.0232-0.05-0.06880.06030.0138-0.08130.034-0.02570.00460.04750.00860.00650.0480.00340.0535
60.63430.603-0.16730.9305-0.13540.5216-0.08430.0205-0.1004-0.11390.0828-0.22140.02290.00430.00430.0619-0.00170.03850.0559-0.00210.0895
Refinement TLS groupSelection details: chain B and resid 156:215)

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