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- PDB-3tka: crystal structure and solution saxs of methyltransferase rsmh fro... -

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Basic information

Entry
Database: PDB / ID: 3tka
Titlecrystal structure and solution saxs of methyltransferase rsmh from E.coli
ComponentsRibosomal RNA small subunit methyltransferase H
KeywordsTRANSFERASE / methyl transferase
Function / homology
Function and homology information


16S rRNA (cytosine1402-N4)-methyltransferase / rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / cytoplasm / cytosol
Similarity search - Function
Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Putative methyltransferase TM0872, insert domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase H
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGao, Z.Q. / Wei, Y. / Zhang, H. / Dong, Y.H.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA.
Authors: Wei, Y. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / Shtykova, E.V. / Xu, J.H. / Liu, Q.S. / Dong, Y.H.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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: Ribosomal RNA small subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9819
Polymers38,6651
Non-polymers1,3168
Water2,612145
1
A: Ribosomal RNA small subunit methyltransferase H
hetero molecules

A: Ribosomal RNA small subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,96218
Polymers77,3302
Non-polymers2,63216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4290 Å2
ΔGint-109 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.660, 85.660, 107.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribosomal RNA small subunit methyltransferase H / 16S rRNA m(4)C1402 methyltransferase / rRNA (cytosine-N(4)-)-methyltransferase RsmH


Mass: 38664.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: rsmH, mraW, yabC, b0082, JW0080 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60390, 16S rRNA (cytosine1402-N4)-methyltransferase

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Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0M ammonium sulfate, 0.1M Hepes, pH 6.5, 0.5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 10, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 18379 / Num. obs: 18379 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 38.61 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 9.59 / Num. unique all: 896 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WG8

1wg8


Resolution: 2.25→40.111 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 926 5.11 %RANDOM
Rwork0.1843 ---
all0.1868 18379 --
obs0.1868 18115 98.76 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.101 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0167 Å20 Å2-0 Å2
2--1.0167 Å20 Å2
3----2.0333 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 81 145 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092345
X-RAY DIFFRACTIONf_angle_d1.173169
X-RAY DIFFRACTIONf_dihedral_angle_d16.405911
X-RAY DIFFRACTIONf_chiral_restr0.072351
X-RAY DIFFRACTIONf_plane_restr0.005411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.36860.41261310.3159232694
2.3686-2.5170.25571290.2344245599
2.517-2.71130.27551350.2165245299
2.7113-2.98410.28921380.2044245899
2.9841-3.41570.22541370.18692477100
3.4157-4.30260.20611390.15192490100
4.3026-40.1170.1991170.16572531100
Refinement TLS params.Method: refined / Origin x: 30.5892 Å / Origin y: 16.7012 Å / Origin z: 15.1349 Å
111213212223313233
T0.1686 Å2-0.0124 Å20.0329 Å2-0.1578 Å20.0344 Å2--0.1666 Å2
L1.2951 °2-0.2862 °20.0506 °2-3.7794 °20.0261 °2--2.4331 °2
S0.1644 Å °0.0142 Å °-0.0146 Å °0.0146 Å °-0.1903 Å °-0.0484 Å °0.0087 Å °0.0915 Å °0.017 Å °
Refinement TLS groupSelection details: all

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