[English] 日本語
Yorodumi
- PDB-2jug: Multienzyme Docking in Hybrid Megasynthetases -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jug
TitleMultienzyme Docking in Hybrid Megasynthetases
ComponentsTubC protein
KeywordsBIOSYNTHETIC PROTEIN / docking domain / dimer / nonribosomal peptide synthetase / tubulysin / Ligase / Phosphopantetheine
Function / homology
Function and homology information


toxin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / catalytic activity / phosphopantetheine binding / cytosol
Similarity search - Function
Non-ribosomal peptide synthase, adenylation domain / TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain ...Non-ribosomal peptide synthase, adenylation domain / TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Arc Repressor Mutant, subunit A / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAngiococcus disciformis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRichter, C.D. / Nietlispach, D. / Broadhurst, R.W. / Weissman, K.J.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Multienzyme docking in hybrid megasynthetases
Authors: Richter, C.D. / Nietlispach, D. / Broadhurst, R.W. / Weissman, K.J.
History
DepositionAug 24, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TubC protein
B: TubC protein


Theoretical massNumber of molelcules
Total (without water)16,2532
Polymers16,2532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein TubC protein


Mass: 8126.371 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Angiococcus disciformis (bacteria) / Genus: Cystobacter / Strain: An d48 / Gene: tubC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q5ZPA9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the N-terminal docking domain of the TubC subunit of the hybrid non-ribosomal peptide synthetase/polyketide synthase that makes tubulysin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1323D 13C-separated 12C-selected NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11013D HNCO
11113D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] TubCdd, 20 uM TSP, 0.1 % sodium azide, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] TubCdd, 20 uM TSP, 0.1 % sodium azide, 50 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM TubCdd, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTubCdd[U-100% 13C; U-100% 15N]1
20 uMTSP1
0.1 %sodium azide1
50 mMsodium phosphate1
100 mMsodium chloride1
0.5 mMTubCdd-1[U-100% 13C; U-100% 15N]2
20 uMTSP2
0.1 %sodium azide2
50 mMsodium phosphate2
100 mMsodium chloride2
0.5 mMTubCdd-22
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
AzaraBoucherprocessing
CcpNmr Analysis1.0.15Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides and Lauechemical shift assignment
CcpNmr Analysis1.0.15Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides and Lauepeak picking
CcpNmr Analysis1.0.15Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides and Lauedata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: simulated annealing using Aria 1.2
NMR constraintsNOE constraints total: 1987 / NOE intraresidue total count: 652 / NOE long range total count: 269 / NOE medium range total count: 449 / NOE sequential total count: 596 / Hydrogen bond constraints total count: 34 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 53 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.049 Å / Distance rms dev error: 0.01 Å

+
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