[English] 日本語
Yorodumi
- PDB-6wtf: Structure of radical S-adenosylmethionine methyltransferase, TsrM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wtf
TitleStructure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora setae with tryptophan substrate and SAM analog (aza-SAM) bound
ComponentsTryptophan-C2-methyltransferase containing B12-binding domain
KeywordsTRANSFERASE / Radical SAM / Cobalamin / FeS cluster / methyltransferase
Function / homology
Function and homology information


cobalamin binding / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Tryptophan 2-C-methyltransferase / : / Radical SAM, alpha/beta horseshoe / B12 binding domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
COBALAMIN / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / IRON/SULFUR CLUSTER / TRYPTOPHAN / Uncharacterized protein
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKnox, H.L. / Chen, P.Y.-T. / Drennan, C.L. / Booker, S.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-12259 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-126982 United States
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Structural basis for non-radical catalysis by TsrM, a radical SAM methylase.
Authors: Knox, H.L. / Chen, P.Y. / Blaszczyk, A.J. / Mukherjee, A. / Grove, T.L. / Schwalm, E.L. / Wang, B. / Drennan, C.L. / Booker, S.J.
History
DepositionMay 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophan-C2-methyltransferase containing B12-binding domain
B: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,80910
Polymers128,2732
Non-polymers4,5358
Water6,792377
1
A: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4045
Polymers64,1371
Non-polymers2,2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area19720 Å2
MethodPISA
2
B: Tryptophan-C2-methyltransferase containing B12-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4045
Polymers64,1371
Non-polymers2,2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.355, 103.085, 105.757
Angle α, β, γ (deg.)90.000, 94.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 165 or resid 180...
21(chain B and (resid 2 through 360 or resid 362...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain A and (resid 2 through 165 or resid 180...AA2 - 1652 - 165
12PROPROTHRTHR(chain A and (resid 2 through 165 or resid 180...AA180 - 360180 - 360
13ARGARGPROPRO(chain A and (resid 2 through 165 or resid 180...AA362 - 517362 - 517
14HISHISGLUGLU(chain A and (resid 2 through 165 or resid 180...AA525 - 563525 - 563
21SERSERTHRTHR(chain B and (resid 2 through 360 or resid 362...BB2 - 3602 - 360
22ARGARGPROPRO(chain B and (resid 2 through 360 or resid 362...BB362 - 483362 - 483
23TRPTRPPROPRO(chain B and (resid 2 through 360 or resid 362...BB495 - 517495 - 517
24HISHISGLUGLU(chain B and (resid 2 through 360 or resid 362...BB525 - 563525 - 563

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Tryptophan-C2-methyltransferase containing B12-binding domain


Mass: 64136.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: KSE_17820 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N8S5

-
Non-polymers , 5 types, 385 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M tri-sodium citrate, pH 5.6, 20% (v/v) isopropanol, 20% (w/v) PEG 4000, and 0.05 M nickel (II) dichloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 53942 / % possible obs: 97.1 % / Redundancy: 4.8 % / CC1/2: 0.8 / Net I/σ(I): 6.47
Reflection shellResolution: 2.19→2.27 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 4655 / CC1/2: 0.8 / Rpim(I) all: 0.28

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WTE

6wte


Resolution: 2.19→46.92 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2689 4.98 %
Rwork0.211 51253 -
obs0.2129 53942 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 23.4202 Å2 / Biso min: 12.61 Å2
Refinement stepCycle: final / Resolution: 2.19→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8503 0 282 377 9162
Biso mean--18.35 23.18 -
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049037
X-RAY DIFFRACTIONf_angle_d0.67212331
X-RAY DIFFRACTIONf_dihedral_angle_d22.0483440
X-RAY DIFFRACTIONf_chiral_restr0.0451323
X-RAY DIFFRACTIONf_plane_restr0.0041679
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5095X-RAY DIFFRACTION4.633TORSIONAL
12B5095X-RAY DIFFRACTION4.633TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.230.35431370.28982567270494
2.23-2.270.38441360.33182731286798
2.27-2.320.31561410.26772694283598
2.32-2.370.3081450.24762747289298
2.37-2.420.28691470.2342698284598
2.42-2.480.29351460.24262693283998
2.48-2.550.30911350.23742716285197
2.55-2.620.30381460.22912716286298
2.62-2.710.23621360.22732652278896
2.71-2.810.27511440.2292738288298
2.81-2.920.29281430.24122682282598
2.92-3.050.29491450.2262723286898
3.05-3.210.24761380.22372717285598
3.21-3.410.24231390.21492694283396
3.41-3.680.2421450.19482697284297
3.68-4.050.21251420.17072682282497
4.05-4.630.17521440.14982716286097
4.63-5.830.15951410.16132684282596
5.83-46.920.21111390.18822706284595

+
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