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- PDB-5hw4: Crystal structure of Escherichia coli 16S rRNA methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5hw4
TitleCrystal structure of Escherichia coli 16S rRNA methyltransferase RsmI in complex with AdoMet
ComponentsRibosomal RNA small subunit methyltransferase I
KeywordsTRANSFERASE / RNA methylation / AdoMet-dependent methyltransferase / ribosome P-site
Function / homology
Function and homology information


16S rRNA (cytidine1402-2'-O)-methyltransferase / : / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm
Similarity search - Function
SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases ...SAM-dependent methyltransferase RsmI, conserved site / RsmI AdoMet-dependent methyltransferase protein family signature. / rRNA small subunit methyltransferase I / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase I
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.211 Å
AuthorsZhao, M. / Zhang, H. / Dong, Y. / Gong, Y.
CitationJournal: Plos One / Year: 2016
Title: Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI
Authors: Zhao, M. / Zhang, H. / Liu, G. / Wang, L. / Wang, J. / Gao, Z. / Dong, Y. / Zhang, L. / Gong, Y.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,9376
Polymers81,7423
Non-polymers1,1953
Water5,603311
1
A: Ribosomal RNA small subunit methyltransferase I
B: Ribosomal RNA small subunit methyltransferase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2914
Polymers54,4942
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-12 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: Ribosomal RNA small subunit methyltransferase I
hetero molecules

C: Ribosomal RNA small subunit methyltransferase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2914
Polymers54,4942
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4180 Å2
ΔGint-15 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.923, 155.270, 54.604
Angle α, β, γ (deg.)90.00, 93.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase I / / 16S rRNA 2'-O-ribose C1402 methyltransferase / rRNA (cytidine-2'-O-)-methyltransferase RsmI


Mass: 27247.191 Da / Num. of mol.: 3 / Fragment: UNP residues 12-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rsmI, yraL, b3146, JW3115 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P67087, 16S rRNA (cytidine1402-2'-O)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M DL-Malic acid, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 46162 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.535 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KWP

3kwp


Resolution: 2.211→34.943 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2329 5.05 %Random selection
Rwork0.2026 ---
obs0.204 46142 92.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53 Å2
Refinement stepCycle: LAST / Resolution: 2.211→34.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 81 311 5582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085367
X-RAY DIFFRACTIONf_angle_d1.1077291
X-RAY DIFFRACTIONf_dihedral_angle_d15.9282000
X-RAY DIFFRACTIONf_chiral_restr0.047858
X-RAY DIFFRACTIONf_plane_restr0.005934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2108-2.25590.27381310.2692228X-RAY DIFFRACTION80
2.2559-2.3050.30171420.2432718X-RAY DIFFRACTION98
2.305-2.35860.25021470.2392745X-RAY DIFFRACTION98
2.3586-2.41760.29941380.24032721X-RAY DIFFRACTION98
2.4176-2.48290.25161530.23132749X-RAY DIFFRACTION98
2.4829-2.55590.28541370.22022718X-RAY DIFFRACTION98
2.5559-2.63840.26971380.23122736X-RAY DIFFRACTION98
2.6384-2.73270.25971550.22732780X-RAY DIFFRACTION98
2.7327-2.8420.22521240.22022703X-RAY DIFFRACTION98
2.842-2.97130.231590.21852704X-RAY DIFFRACTION97
2.9713-3.12790.26271460.20592655X-RAY DIFFRACTION95
3.1279-3.32370.25581470.20752629X-RAY DIFFRACTION94
3.3237-3.58010.21111240.18852620X-RAY DIFFRACTION92
3.5801-3.93990.22231300.18122458X-RAY DIFFRACTION87
3.9399-4.5090.18821170.17752238X-RAY DIFFRACTION80
4.509-5.6770.19691370.18912276X-RAY DIFFRACTION82
5.677-500.22981040.19942135X-RAY DIFFRACTION75

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