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- PDB-1sqg: The crystal structure of the E. coli Fmu apoenzyme at 1.65 A reso... -

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Basic information

Entry
Database: PDB / ID: 1sqg
TitleThe crystal structure of the E. coli Fmu apoenzyme at 1.65 A resolution
ComponentsSUN protein
KeywordsTRANSFERASE / Rossmann-fold / mixed beta sheet / methyltransferase-fold / RNA-binding domain
Function / homology
Function and homology information


16S rRNA (cytosine967-C5)-methyltransferase / rRNA (cytosine-C5-)-methyltransferase activity / rRNA base methylation / regulation of DNA-templated transcription / RNA binding / cytosol
Similarity search - Function
rRNA small subunit methyltransferase B / rRNA small subunit methyltransferase B, enterobacteriaceae / : / Helix hairpin bin / N-utilizing Substance Protein B Homolog; Chain A / NusB-like / Sun protein; domain 3 / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily ...rRNA small subunit methyltransferase B / rRNA small subunit methyltransferase B, enterobacteriaceae / : / Helix hairpin bin / N-utilizing Substance Protein B Homolog; Chain A / NusB-like / Sun protein; domain 3 / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / : / Methyltr_RsmF/B-like, ferredoxin-like domain / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 / Helix Hairpins / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFoster, P.G. / Nunes, C.R. / Greene, P. / Moustakas, D. / Stroud, R.M.
CitationJournal: Structure / Year: 2003
Title: The First Structure of an RNA m5C Methyltransferase, Fmu, Provides Insight into Catalytic Mechanism and Specific Binding of RNA Substrate
Authors: Foster, P.G. / Nunes, C.R. / Greene, P. / Moustakas, D. / Stroud, R.M.
History
DepositionMar 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SUN protein


Theoretical massNumber of molelcules
Total (without water)48,4081
Polymers48,4081
Non-polymers00
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.672, 48.695, 86.802
Angle α, β, γ (deg.)90.00, 108.65, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein SUN protein / FMU protein


Mass: 48408.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SUN, FMU, FMV, RSMB, B3289 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36929
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG4000, Tris-HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.921 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 1.65→31.4 Å / Num. all: 56917 / Num. obs: 56794 / % possible obs: 98.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.351 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25721 2799 5 %RANDOM
Rwork0.2229 ---
obs0.22461 53354 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.991 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.03 Å2
2--1.26 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 0 390 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213364
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9534576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6113423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85915612
X-RAY DIFFRACTIONr_chiral_restr0.10.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022578
X-RAY DIFFRACTIONr_nbd_refined0.2490.31789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.515
X-RAY DIFFRACTIONr_mcbond_it0.5221.52114
X-RAY DIFFRACTIONr_mcangle_it0.96223390
X-RAY DIFFRACTIONr_scbond_it1.81531250
X-RAY DIFFRACTIONr_scangle_it2.8154.51186
LS refinement shellResolution: 1.65→1.695 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 186
Rwork0.25 3299
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)
12.0430.6584-0.78271.8362-0.04122.3890.0758-0.06310.0187-0.0306-0.0468-0.056-0.20330.2432-0.0290.0405-0.0224-0.00960.0262-0.00850.06657.95511.719229.4494
20.5959-0.27440.02370.82531.49546.75340.00430.1092-0.0227-0.0537-0.0406-0.07360.23940.11460.03630.0774-0.01140.01430.0017-0.00380.0994-4.0493-9.78215.0158
31.7697-0.4088-0.47961.16891.63493.9137-0.00670.3866-0.0529-0.0899-0.4720.3139-0.0253-1.30650.47860.0914-0.01540.00190.4536-0.160.1628-22.1831-5.219118.8481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1445 - 144
2X-RAY DIFFRACTION2AA145 - 232145 - 232
3X-RAY DIFFRACTION3AA233 - 428233 - 428

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