[English] 日本語
Yorodumi
- PDB-1sqf: The crystal structure of E. coli Fmu binary complex with S-Adenos... -

+
Open data


ID or keywords:

Loading...

-
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 proteinSUN domain
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
Components

#1: Protein SUN protein / SUN domain / 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 / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more