[English] 日本語
Yorodumi
- PDB-3e5y: Crystal structure of TrmH family RNA methyltransferase from Burkh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e5y
TitleCrystal structure of TrmH family RNA methyltransferase from Burkholderia pseudomallei
ComponentsTrmH family RNA methyltransferase
KeywordsTRANSFERASE / SSGCID / protein knot / deCODE / RNA methyltransferase / Methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 305 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of TrmH family RNA methyltransferase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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: TrmH family RNA methyltransferase
B: TrmH family RNA methyltransferase


Theoretical massNumber of molelcules
Total (without water)35,5462
Polymers35,5462
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-8 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.724, 80.532, 80.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TrmH family RNA methyltransferase / RNA methyltransferase / TrmH family / group 2


Mass: 17773.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 305 (bacteria)
Gene: BURPS305_4843 / Production host: Escherichia coli (E. coli) / References: UniProt: A4LJP7, UniProt: A0A0E1SBH3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 289 K / pH: 8.5
Details: PACT sparse matrix screen G10 and H10; 20% PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M BisTris propane, pH 7.5 or 8.5; 27.6 mg/mL protein; Crystal ID 109613h10, VAPOR DIFFUSION, ...Details: PACT sparse matrix screen G10 and H10; 20% PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M BisTris propane, pH 7.5 or 8.5; 27.6 mg/mL protein; Crystal ID 109613h10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12194 / % possible obs: 97.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3 / % possible all: 95.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.4.0067refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J85

1j85


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 8.678 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 592 4.9 %RANDOM
Rwork0.213 ---
obs0.215 12162 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---0.97 Å20 Å2
3---2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 162 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222407
X-RAY DIFFRACTIONr_bond_other_d0.0020.021690
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.943272
X-RAY DIFFRACTIONr_angle_other_deg1.47534025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.2445294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.17821.825126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.51483
X-RAY DIFFRACTIONr_mcbond_other0.1531.5593
X-RAY DIFFRACTIONr_mcangle_it1.57422375
X-RAY DIFFRACTIONr_scbond_it2.3153924
X-RAY DIFFRACTIONr_scangle_it3.7434.5897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 35 -
Rwork0.274 802 -
obs--91.58 %

+
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