[English] 日本語
Yorodumi
- PDB-2mr7: apo structure of the Peptidyl Carrier Protein Domain 7 of the tei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mr7
Titleapo structure of the Peptidyl Carrier Protein Domain 7 of the teicoplanin producing Non-ribosomal peptide synthetase
ComponentsNon-ribosomal peptide synthetase
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / peptidyl carrier protein
Function / homology
Function and homology information


amide biosynthetic process / : / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsHaslinger, K. / Maximowitsch, E. / Redfield, C. / Cryle, M.J.
CitationJournal: Proteins / Year: 2015
Title: Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis.
Authors: Haslinger, K. / Redfield, C. / Cryle, M.J.
History
DepositionJul 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)9,6311
Polymers9,6311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein Non-ribosomal peptide synthetase


Mass: 9631.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Strain: 1867 / Gene: tcp12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold (DE3) / References: UniProt: Q70AZ6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1222D 1H-1H NOESY
1332D 1H-1H NOESY
1413D 1H-13C NOESY
1522D DQF-COSY
1612D 1H-15N HSQC
1712D 1H-13C HSQC
1813D CBCA(CO)NH
1913D HNCO
11013D HNCA
11113D HN(CA)CB
11213D HBHA(CO)NH
11313D HN(CO)CA
11413D (H)CCH-TOCSY
11513D HNCCCONH
11613D CBCANH
11722D 1H-1H TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1350-500 uM [U-100% 13C; U-100% 15N] PCP7T, 50 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
2500 uM PCP7T, 50 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
3500 uM PCP7T, 50 mM TRIS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMPCP7T-1[U-100% 13C; U-100% 15N]350-5001
50 mMTRIS-21
500 uMPCP7T-32
50 mMTRIS-42
500 uMPCP7T-53
50 mMTRIS-63
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Oxford OMEGAOxfordOMEGA6001
Oxford OMEGAOxfordOMEGA7502
Oxford OMEGAOxfordOMEGA9503

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.3.1CCPNchemical shift assignment
CcpNmr Analysis2.3.1CCPNpeak picking
YASARA2YASARA Biosciences GmbHprocessing
YASARA2YASARA Biosciences GmbHrefinement
YASARA2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
YASARA2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
YASARA2YASARA Biosciences GmbHprocessing
YASARA2YASARA Biosciences GmbHrefinement
YASARA2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
YASARA2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
WHAT IFVrienddata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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