[English] 日本語
Yorodumi
- PDB-3m6u: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m6u
TitleMulti-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group 43
ComponentsrRNA methylase
KeywordsTRANSFERASE / rRNA methyltransferase / 5-methylcytidine / RsmF / AdoMet / Multi-specific / Methyltransferase
Function / homology
Function and homology information


16S rRNA (cytosine1407-C5)-methyltransferase / RNA methylation / RNA methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / RNA binding / cytoplasm
Similarity search - Function
: / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Sun protein; domain 3 / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase ...: / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Sun protein; domain 3 / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / 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 / Roll / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase F
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.402 Å
AuthorsDemirci, H. / Larsen, H.G.L. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.
CitationJournal: Rna / Year: 2010
Title: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
Authors: Demirci, H. / Larsen, L.H. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rRNA methylase
B: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1416
Polymers101,7572
Non-polymers3844
Water26,7701486
1
A: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0713
Polymers50,8791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0713
Polymers50,8791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.979, 70.979, 186.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein rRNA methylase


Mass: 50878.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RsmF minus / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1387 / Plasmid: pLJ102 / Production host: Escherichia coli (E. coli) / Strain (production host): CP79
References: UniProt: Q5SII2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1486 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6.6
Details: 20% (w/v) PEG3350, 200 mM sodium sulfate decahydrate (pH 6.6), microbatch under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2008 / Details: Variable vertical and horizontal slits
RadiationMonochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 162166 / % possible obs: 90.1 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.065 / Χ2: 1.681 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.455.40.586130910.69472.6
1.45-1.515.50.421134570.7775.1
1.51-1.585.70.277139410.74777.6
1.58-1.665.90.19144820.82980.9
1.66-1.769.50.158176201.08997.9
1.76-1.910.20.125178731.43999.5
1.9-2.0910.10.113178032.45198.8
2.09-2.3910.50.092178942.30399.4
2.39-3.0211.80.07179941.96999.9
3.02-3011.50.049180112.08399.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FRX

2frx


Resolution: 1.402→29.962 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.88 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 8148 5.03 %
Rwork0.169 --
obs0.17 161955 90.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.435 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 139.66 Å2 / Biso mean: 26.617 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.038 Å2-0 Å20 Å2
2---0.038 Å20 Å2
3---0.075 Å2
Refinement stepCycle: LAST / Resolution: 1.402→29.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 20 1486 8230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096993
X-RAY DIFFRACTIONf_angle_d1.2249531
X-RAY DIFFRACTIONf_chiral_restr0.0781005
X-RAY DIFFRACTIONf_plane_restr0.0071258
X-RAY DIFFRACTIONf_dihedral_angle_d16.8892558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.402-1.4180.2632070.2274149435672
1.418-1.4350.2462160.224091430772
1.435-1.4520.2512560.2194173442973
1.452-1.470.2322060.2044195440174
1.47-1.490.2312170.2244262447975
1.49-1.510.2262260.1844352457876
1.51-1.5320.2132310.1874321455277
1.532-1.5550.2112420.1664402464478
1.555-1.5790.192600.1644494475479
1.579-1.6050.1812540.1554497475180
1.605-1.6330.182520.1554557480981
1.633-1.6620.1882230.1624691491482
1.662-1.6940.23020.1665465576796
1.694-1.7290.2123140.1595647596199
1.729-1.7660.1943030.1645611591499
1.766-1.8070.1812820.1625651593399
1.807-1.8530.183010.1595678597999
1.853-1.9030.1832910.1765634592599
1.903-1.9590.2313160.2065465578196
1.959-2.0220.1962870.16856795966100
2.022-2.0940.1842920.15957065998100
2.094-2.1780.182930.16256515944100
2.178-2.2770.2172810.1785612589398
2.277-2.3970.1913240.16656695993100
2.397-2.5470.1842930.16857035996100
2.547-2.7440.1833190.16456725991100
2.744-3.020.1893060.16756795985100
3.02-3.4560.1882850.16557356020100
3.456-4.3520.1682810.14357196000100
4.352-29.9690.1542880.1635647593598
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)
10.2480.1010.24880.38220.12350.4792-0.11210.00560.0646-0.08020.03310.034-0.1839-0.01690.07190.13290.0187-0.03070.08460.01350.097412.28539.1287180.6658
20.0707-0.0433-0.00840.3125-0.02170.0922-0.0207-0.0688-0.0407-0.00820.01360.03140.002-0.0417-0.00030.05280.0016-0.00470.08780.02390.085614.264121.9299189.8411
30.4904-0.47860.42131.3929-0.25160.5219-0.156-0.10910.05660.24360.1195-0.0752-0.1694-0.09540.02520.12180.0512-0.01270.1074-0.00080.081920.212134.4877200.5039
40.55830.12750.5530.0988-0.04862.16880.1811-0.0007-0.30460.0122-0.0001-0.16960.6350.0573-0.16970.23110.0043-0.06290.07810.02910.203417.8404-3.8871182.6614
50.586-0.19890.39620.24330.05030.91720.07970.0361-0.096-0.07660.00310.02540.1172-0.0109-0.08070.1226-0.024-0.02190.08510.01590.10649.81577.5885174.1013
60.1938-0.1394-0.27010.47470.21320.5512-0.1132-0.0002-0.06120.090.0420.06680.1739-0.02450.06490.1257-0.01730.02820.08420.01580.1018-23.4093-3.6759201.6773
70.06350.08-0.05790.2707-0.0070.0748-0.01780.06520.03750.00870.01580.0297-0.0013-0.04810.0030.0589-0.00070.00170.09650.02710.095-21.380413.4466192.4587
80.69870.5884-0.56581.6211-0.42960.6572-0.15650.1241-0.0647-0.26260.1152-0.06160.1915-0.09460.03510.1203-0.04940.01330.1015-0.00510.0761-14.80510.6607182.0436
90.6603-0.0332-0.73510.0815-0.14842.38250.23920.02280.30440.02440.0055-0.0845-0.63790.0441-0.21330.2084-0.00650.05390.07130.01950.18-17.514539.092199.1478
100.56420.2451-0.35330.2708-0.02540.88630.0758-0.02590.10090.07910.01160.0317-0.1154-0.0139-0.08540.1250.0270.02310.08550.01620.1095-25.66627.9143208.215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 6:71A6 - 71
2X-RAY DIFFRACTION2chain A and resseq 72:198A72 - 198
3X-RAY DIFFRACTION3chain A and resseq 201:310A201 - 310
4X-RAY DIFFRACTION4chain A and resseq 311:341A311 - 341
5X-RAY DIFFRACTION5chain A and resseq 342:459A342 - 459
6X-RAY DIFFRACTION6chain B and resseq 6:71B6 - 71
7X-RAY DIFFRACTION7chain B and resseq 72:198B72 - 198
8X-RAY DIFFRACTION8chain B and resseq 204:309B204 - 309
9X-RAY DIFFRACTION9chain B and resseq 310:341B310 - 341
10X-RAY DIFFRACTION10chain B and resseq 342:459B342 - 459

+
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