[English] 日本語
Yorodumi
- PDB-5f8f: Rv2258c-SFG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f8f
TitleRv2258c-SFG
ComponentsMethyltransferase
KeywordsTRANSFERASE / methyltransferase / Class I / sinefungin / S-adenosyl-L-homocysteine / complex
Function / homology
Function and homology information


peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / cellular response to hypoxia / plasma membrane
Similarity search - Function
: / Rv2258c-like winged HTH domain / : / Methyltransferase domain / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / S-adenosylmethionine-dependent methyltransferase Rv2258c
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsIm, H.N. / Suh, S.W.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase
Authors: Im, H.N. / Kim, H.S. / An, D.R. / Jang, J.Y. / Kim, J. / Yoon, H.J. / Yang, J.K. / Suh, S.W.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8929
Polymers121,4723
Non-polymers1,4206
Water12,556697
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0207
Polymers80,9812
Non-polymers1,0395
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-67 kcal/mol
Surface area28170 Å2
MethodPISA
2
C: Methyltransferase
hetero molecules

C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7444
Polymers80,9812
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area7360 Å2
ΔGint-65 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.958, 141.118, 96.970
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Methyltransferase / Possible transcriptional regulatory protein


Mass: 40490.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2258c, LH57_12310 / Production host: Escherichia coli (E. coli) / References: UniProt: O53532
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: sodium malonate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 113690 / % possible obs: 99.9 % / Redundancy: 4 % / Net I/σ(I): 28.8
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.93 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 5682 5 %RANDOM
Rwork0.1925 ---
obs0.194 107815 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.4 Å2 / Biso mean: 37.958 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å2-0 Å21.2 Å2
2---1.42 Å2-0 Å2
3----2.86 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8000 0 99 697 8796
Biso mean--44.18 44.08 -
Num. residues----1068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198241
X-RAY DIFFRACTIONr_bond_other_d0.0030.027816
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.97911187
X-RAY DIFFRACTIONr_angle_other_deg1.0033.00517922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67951065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39323.754349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.171151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2671558
X-RAY DIFFRACTIONr_chiral_restr0.0810.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021836
X-RAY DIFFRACTIONr_mcbond_it2.033.6094278
X-RAY DIFFRACTIONr_mcbond_other2.033.6094278
X-RAY DIFFRACTIONr_mcangle_it2.9235.3985337
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 427 -
Rwork0.276 7952 -
all-8379 -
obs--99.93 %

+
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