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- PDB-1sqf: The crystal structure of E. coli Fmu binary complex with S-Adenos... -

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Basic information

Entry
Database: PDB / ID: 1sqf
TitleThe crystal structure of E. coli Fmu binary complex with S-Adenosylmethionine at 2.1 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
S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SUN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8072
Polymers48,4081
Non-polymers3981
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.407, 49.282, 86.920
Angle α, β, γ (deg.)90.00, 109.47, 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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
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: 2→31.55 Å / Num. all: 31507 / Num. obs: 31286 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.537 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27635 2226 8.2 %RANDOM
Rwork0.22648 ---
obs0.23063 24808 99.83 %-
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: 22.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å2-0.36 Å2
2--1.08 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 27 115 3431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213393
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.9644619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8583424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05515608
X-RAY DIFFRACTIONr_chiral_restr0.1330.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022583
X-RAY DIFFRACTIONr_nbd_refined0.2960.31803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.40.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.52
X-RAY DIFFRACTIONr_mcbond_it1.0811.52122
X-RAY DIFFRACTIONr_mcangle_it1.77723402
X-RAY DIFFRACTIONr_scbond_it3.08531271
X-RAY DIFFRACTIONr_scangle_it4.4134.51217
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 173
Rwork0.26 1861
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)
14.5763-3.2504-2.32644.83092.15643.8690.54580.48440.5545-0.369-0.3372-0.3861-0.3602-0.4101-0.20860.0950.04720.05780.09730.08080.1534-21.43613.080111.6023
22.9332-0.89890.69833.67450.20385.5684-0.17080.5462-0.3255-0.22330.09970.08490.48910.29120.07120.0154-0.0212-0.01840.1175-0.03850.0679-8.7651-7.13456.7794
32.67860.4780.73841.8621-0.88557.71880.0451-0.2977-0.09110.2994-0.09040.2370.4249-0.42110.04530.1868-0.00970.00270.01190.010.0852-10.7451-9.351735.705
42.99480.6538-0.24750.9389-0.08342.3959-0.074-0.0551-0.14420.17170.0822-0.21060.30730.7166-0.00820.12390.114-0.03440.2027-0.01890.11028.4097-5.524522.4717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1445 - 144
2X-RAY DIFFRACTION2AA145 - 172145 - 172
3X-RAY DIFFRACTION3AA173 - 232173 - 232
4X-RAY DIFFRACTION4AA233 - 429233 - 429

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