[English] 日本語
Yorodumi
- PDB-7kdy: Crystal structure of Streptomyces tokunonesis TokK with hydroxyco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kdy
TitleCrystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)-pantetheinylated carbapenam
ComponentsMethyltransferase TokK
KeywordsTRANSFERASE / Radical SAM / Cobalamin / [4Fe-4S] cluster / FeS cluster / methyltransferase / B12 / beta-lactam antibiotic synthesis
Function / homology
Function and homology information


cobalamin binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / 4 iron, 4 sulfur cluster binding / methylation / metal ion binding / cytosol
Similarity search - Function
Carbapenem intermediate methyltransferase ThnK-like / : / Radical SAM, alpha/beta horseshoe / Cobalamin-binding domain / B12 binding domain / Elp3/MiaB/NifB / Cobalamin-binding domain superfamily / Elongator protein 3, MiaB family, Radical SAM / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain ...Carbapenem intermediate methyltransferase ThnK-like / : / Radical SAM, alpha/beta horseshoe / Cobalamin-binding domain / B12 binding domain / Elp3/MiaB/NifB / Cobalamin-binding domain superfamily / Elongator protein 3, MiaB family, Radical SAM / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Radical SAM core domain profile. / Radical SAM / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / : / METHIONINE / IRON/SULFUR CLUSTER / Chem-WCD / Cobalamin-dependent radical SAM methyltransferase TokK
Similarity search - Component
Biological speciesStreptomyces tokunonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsKnox, H.L. / Booker, S.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-12259 United States
CitationJournal: Nature / Year: 2022
Title: Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
Authors: Knox, H.L. / Sinner, E.K. / Townsend, C.A. / Boal, A.K. / Booker, S.J.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Methyltransferase TokK
B: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,85417
Polymers154,9172
Non-polymers4,93715
Water21,4921193
1
A: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1439
Polymers77,4591
Non-polymers2,6848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase TokK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7118
Polymers77,4591
Non-polymers2,2537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.503, 132.817, 155.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 168 or resid 170...
21(chain B and (resid 9 through 168 or resid 170...

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
11GLYGLYPROPRO(chain A and (resid 9 through 168 or resid 170...AA9 - 1689 - 168
12LEULEUTYRTYR(chain A and (resid 9 through 168 or resid 170...AA170 - 208170 - 208
13CYSCYSCYSCYS(chain A and (resid 9 through 168 or resid 170...AA210210
14THRTHRPHEPHE(chain A and (resid 9 through 168 or resid 170...AA222 - 424222 - 424
15METMETGLYGLY(chain A and (resid 9 through 168 or resid 170...AA426 - 454426 - 454
16TYRTYRMETMET(chain A and (resid 9 through 168 or resid 170...AA456 - 498456 - 498
17SERSERLEULEU(chain A and (resid 9 through 168 or resid 170...AA500 - 672500 - 672
18HOHHOHHOHHOH(chain A and (resid 9 through 168 or resid 170...AR901
21GLYGLYPROPRO(chain B and (resid 9 through 168 or resid 170...BB9 - 1689 - 168
22LEULEUTYRTYR(chain B and (resid 9 through 168 or resid 170...BB170 - 208170 - 208
23CYSCYSMETMET(chain B and (resid 9 through 168 or resid 170...BB210 - 220210 - 220
24THRTHRPHEPHE(chain B and (resid 9 through 168 or resid 170...BB222 - 424222 - 424
25METMETGLYGLY(chain B and (resid 9 through 168 or resid 170...BB426 - 454426 - 454
26TYRTYRMETMET(chain B and (resid 9 through 168 or resid 170...BB456 - 498456 - 498
27SERSERASPASP(chain B and (resid 9 through 168 or resid 170...BB500 - 567500 - 567
28ALAALALEULEU(chain B and (resid 9 through 168 or resid 170...BB572 - 672572 - 672
29HOHHOHHOHHOH(chain B and (resid 9 through 168 or resid 170...BS901

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Methyltransferase TokK


Mass: 77458.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tokunonensis (bacteria) / Gene: tokK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B9HEI0

-
Non-polymers , 8 types, 1208 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-WCD / (2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid / (2R)-pantetheinylated carbapenam


Mass: 431.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N3O7S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1193 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, and 18% PEG 8000

-
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: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.939→50 Å / Num. obs: 129910 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 58.5
Reflection shellResolution: 1.94→1.97 Å / Num. unique obs: 6430 / CC1/2: 0.975

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000252295

Resolution: 1.939→44.185 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 3010 1.54 %
Rwork0.1568 192225 -
obs0.1572 129910 77.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.03 Å2 / Biso mean: 24.9169 Å2 / Biso min: 2.14 Å2
Refinement stepCycle: final / Resolution: 1.939→44.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10635 0 297 1193 12125
Biso mean--17.28 31.77 -
Num. residues----1325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411276
X-RAY DIFFRACTIONf_angle_d0.75315372
X-RAY DIFFRACTIONf_chiral_restr0.0471610
X-RAY DIFFRACTIONf_plane_restr0.0052083
X-RAY DIFFRACTIONf_dihedral_angle_d12.9846799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6320X-RAY DIFFRACTION4.572TORSIONAL
12B6320X-RAY DIFFRACTION4.572TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9395-1.97130.2308930.2143599251
1.9713-2.00520.223950.2009604752
2.0052-2.04170.2078950.197605352
2.0417-2.0810.2206950.1927614352
2.081-2.12350.2128970.1861623353
2.1235-2.16960.23521000.1826642055
2.1696-2.22010.23811100.1815659856
2.2201-2.27560.21951110.1711707960
2.2756-2.33710.17681250.1644783867
2.3371-2.40590.21321370.1575870574
2.4059-2.48360.20861560.156966782
2.4836-2.57230.17311640.16491045889
2.5723-2.67530.19361740.1711128796
2.6753-2.7970.18591830.16651164099
2.797-2.94450.19561790.16491167099
2.9445-3.12890.23191820.16611777100
3.1289-3.37040.17771890.160211691100
3.3704-3.70940.18961820.151211736100
3.7094-4.24580.16491790.130511743100
4.2458-5.34780.15281870.126711740100
5.3478-44.1850.16291770.150511708100
Refinement TLS params.Method: refined / Origin x: 3.0467 Å / Origin y: -9.4023 Å / Origin z: -32.9209 Å
111213212223313233
T-0.0795 Å2-0.0778 Å2-0.0691 Å2--0.007 Å2-0.0234 Å2---0.0158 Å2
L0.0667 °2-0.0118 °2-0.0289 °2-0.2218 °2-0.015 °2--0.0198 °2
S0.0345 Å °0.0679 Å °0.0497 Å °0.1324 Å °-0.0227 Å °-0.0366 Å °0.0035 Å °0.022 Å °0.047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 672
2X-RAY DIFFRACTION1allA701 - 1401
3X-RAY DIFFRACTION1allB9 - 672
4X-RAY DIFFRACTION1allB701 - 1101
5X-RAY DIFFRACTION1allS12 - 1365
6X-RAY DIFFRACTION1allC1 - 4

+
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