[English] 日本語
Yorodumi
- PDB-2nxn: T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nxn
TitleT. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11
Components
  • 50S ribosomal protein L11
  • Ribosomal protein L11 methyltransferase
KeywordsTRANSFERASE / S-Adenosyl-L-Methionine dependent methyltransferase / post-translational modification
Function / homology
Function and homology information


protein-lysine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / large ribosomal subunit rRNA binding / methylation / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / Ribosomal protein L11 methyltransferase / : / Sun protein; domain 3 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11 methyltransferase (PrmA) / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / Ribosomal protein L11 methyltransferase / : / Sun protein; domain 3 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11 methyltransferase (PrmA) / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL11 / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDemirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Embo J. / Year: 2007
Title: Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
Authors: Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase
B: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)43,1882
Polymers43,1882
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-20 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.844, 132.844, 46.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Ribosomal protein L11 methyltransferase / L11 Mtase


Mass: 27661.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prmA / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein 50S ribosomal protein L11


Mass: 15526.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rplK, rpl11 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PrmA::tc / References: UniProt: P36238
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25.5 % w/v PEG4000, 120 mM Sodium Acetate, 85mM TRIS, pH 8.5, 15 % v/v glycerol, 4% v/v 1,1,1,3,3,3-Hexafluoro-2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 18545 / Num. obs: 18330 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1766 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1MMS, 2NXC

1mms

2nxc


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.522 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27277 940 5.1 %RANDOM
Rwork0.2202 ---
obs0.22273 17325 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 0 95 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223032
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9824124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4322.881118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5615485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1861524
X-RAY DIFFRACTIONr_chiral_restr0.1180.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022302
X-RAY DIFFRACTIONr_nbd_refined0.2270.21275
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.27
X-RAY DIFFRACTIONr_mcbond_it0.7331.51984
X-RAY DIFFRACTIONr_mcangle_it1.17223081
X-RAY DIFFRACTIONr_scbond_it1.74231205
X-RAY DIFFRACTIONr_scangle_it2.7554.51043
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 79 -
Rwork0.257 1242 -
obs-1242 97.28 %
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)
117.39285.1966-8.706220.17128.964426.0236-0.66991.9915-0.7693-4.27360.9259-1.9213-1.24270.2371-0.256-0.052-0.2140.63570.18420.21210.232951.01181.4409-14.6725
278.5914.8641-36.24097.0775-1.012324.00682.9385-0.47540.95611.1011-0.61841.2352-2.17921.6631-2.320.10380.15580.27260.1608-0.03220.10232.984663.2248-12.2403
32.35330.17630.19873.5491-0.5972.21-0.0281-0.0043-0.0274-0.1248-0.1596-0.412-0.03760.35660.1878-0.16350.0110.0167-0.04580.0555-0.148216.00377.2642-0.601
46.9219-3.0899-0.455513.00370.11676.86190.15360.91640.1583-0.24050.2045-0.85470.19240.7535-0.3581-0.37530.04140.04280.13540.13670.240841.711274.9088-0.8597
519.3773-3.26535.911417.60283.754223.86540.33970.81891.00070.65590.36160.675-1.58391.7278-0.70130.2156-0.33770.27330.14490.01960.517554.693297.7852-0.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION2A55 - 68
3X-RAY DIFFRACTION3A69 - 254
4X-RAY DIFFRACTION4B1 - 74
5X-RAY DIFFRACTION5B75 - 139

+
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