[English] 日本語
Yorodumi
- PDB-3fyd: Crystal Structure of Dim1 from the thermophilic archeon, Methanoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fyd
TitleCrystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi
ComponentsProbable dimethyladenosine transferase
KeywordsTRANSFERASE / dimethyladenosine transferase / rossmann fold / rRNA methylase / ribosomal assembly / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsScarsdale, J.N. / Musayev, F.N. / Rife, J.P.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
Authors: Pulicherla, N. / Pogorzala, L.A. / Xu, Z. / O Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Sia, E.A. / Culver, G.M. / Rife, J.P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli.
Authors: O'Farrell, H.C. / Scarsdale, J.N. / Rife, J.P.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7966
Polymers30,3161
Non-polymers4805
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.236, 65.906, 61.932
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Probable dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase


Mass: 30316.139 Da / Num. of mol.: 1 / Mutation: K137A, E138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: ksgA, MJ1029 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q58435, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000 (14-16%), 25 mM MES, 50 MM NH2SO4, 7 mM MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2008 / Details: Rigaku Varimax Confocal Optics
RadiationMonochromator: Rigaku Varimax Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→33.1 Å / Num. all: 31119 / Num. obs: 29365 / % possible obs: 94.4 % / Redundancy: 7.06 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.98 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3079 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX+ REFMAC 5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9

1qyr

2h1r

1zq9


Resolution: 1.75→22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.061 / SU ML: 0.087
Isotropic thermal model: TLS for each domain + individual residual isotropic B-factors
Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Structure was initially refined with cartesian annealing with phenix.refine followed by refinement with refmac.
RfactorNum. reflection% reflectionSelection details
Rfree0.22643 2926 10 %RANDOM
Rwork0.17624 ---
obs0.18126 26413 94.37 %-
all-31106 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.42 Å2
2---0.48 Å20 Å2
3---0.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.75→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 25 333 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0110.0222244
X-RAY DIFFRACTIONf_bond_other_d
X-RAY DIFFRACTIONf_angle_refined_deg1.1331.9773051
X-RAY DIFFRACTIONf_angle_other_deg
X-RAY DIFFRACTIONf_dihedral_angle_1_deg5.6795282
X-RAY DIFFRACTIONf_dihedral_angle_2_deg32.70825.481104
X-RAY DIFFRACTIONf_dihedral_angle_3_deg14.47515409
X-RAY DIFFRACTIONf_dihedral_angle_4_deg14.768159
X-RAY DIFFRACTIONf_chiral_restr0.090.2342
X-RAY DIFFRACTIONf_gen_planes_refined0.0050.021686
X-RAY DIFFRACTIONf_gen_planes_other
X-RAY DIFFRACTIONf_nbd_refined0.1970.21118
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined0.3040.21593
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined0.1270.2273
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined0.1880.233
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined0.1330.228
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it4.04141425
X-RAY DIFFRACTIONf_mcbond_other
X-RAY DIFFRACTIONf_mcangle_it4.8762232
X-RAY DIFFRACTIONf_scbond_it8.0448930
X-RAY DIFFRACTIONf_scangle_it9.58410819
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 215 -
Rwork0.225 1861 -
obs--100 %
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)
12.4543-0.40910.80331.0627-0.00441.3465-0.03590.20540.1293-0.20630.009-0.0688-0.07430.00540.0269-0.1397-0.02980.0385-0.16010.0092-0.147818.489921.08121.5406
23.81281.44891.13544.20621.34312.71560.0749-0.26250.0730.4196-0.0692-0.03460.0348-0.0968-0.0057-0.14730.02030.0132-0.13680.0083-0.169841.898623.878246.3464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 180
2X-RAY DIFFRACTION2A192 - 269

+
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