[English] 日本語
Yorodumi
- PDB-7dxo: The mutant of bifunctional thioesterase catalyzing epimerization ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dxo
TitleThe mutant of bifunctional thioesterase catalyzing epimerization and cyclization
ComponentsNon-ribosomal peptide synthetase 4
KeywordsBIOSYNTHETIC PROTEIN / hydrolase fold / thioesterase / epimerization / cyclization
Function / homology
Function and homology information


polyketide biosynthetic process / amide biosynthetic process / organic cyclic compound biosynthetic process / organonitrogen compound biosynthetic process / carboxylic acid metabolic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity
Similarity search - Function
Non-ribosomal peptide synthase / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Non-ribosomal peptide synthase / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase 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 / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / 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 / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Non-ribosomal peptide synthetase 4
Similarity search - Component
Biological speciesStreptomyces abietis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYu, J.H. / Song, J. / Chi, C.B. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877002, 81673332, 81991525, 81573326 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis
Authors: Yu, J. / Juan, S. / Chi, C. / Liu, T. / Geng, T. / Cai, Z. / Dong, W. / Shi, C. / Ma, X. / Zhang, Z. / Ma, X. / Xing, B. / Jin, H. / Zhang, L. / Dong, S. / Yang, D. / Ma, M.
History
DepositionJan 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-ribosomal peptide synthetase 4
B: Non-ribosomal peptide synthetase 4
C: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)90,6153
Polymers90,6153
Non-polymers00
Water3,441191
1
A: Non-ribosomal peptide synthetase 4
B: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)60,4102
Polymers60,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-8 kcal/mol
Surface area21120 Å2
MethodPISA
2
C: Non-ribosomal peptide synthetase 4

C: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)60,4102
Polymers60,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1740 Å2
ΔGint-9 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.959, 117.582, 210.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-310-

HOH

-
Components

#1: Protein Non-ribosomal peptide synthetase 4


Mass: 30204.977 Da / Num. of mol.: 3 / Mutation: S97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces abietis (bacteria) / Gene: nrps4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1J0R317
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe Ala206 in the sequence is different naturally to the published homologues (A0A1J0R317). ...The Ala206 in the sequence is different naturally to the published homologues (A0A1J0R317). Sequence used in this study was derived from Streptomyces strain isolated from a marine coral sample, which has not been deposited to any database at the time of data annotation.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 60% v/v Tacsimate, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.540562 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 2.4→27.13 Å / Num. obs: 33187 / % possible obs: 99.1 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 25.37
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.234 / Num. unique obs: 3325

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CRN

7crn


Resolution: 2.4→5.22 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2801 1987 6 %
Rwork0.2227 31126 -
obs0.2263 33113 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.49 Å2 / Biso mean: 17.8224 Å2 / Biso min: 1.3 Å2
Refinement stepCycle: final / Resolution: 2.4→5.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 0 191 6251
Biso mean---17.26 -
Num. residues----792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.37741420.29012210235299
2.46-2.530.30091420.264322032345100
2.53-2.60.32661420.247522202362100
2.6-2.680.28841390.238321912330100
2.68-2.780.31711450.237621862331100
2.78-2.890.29511460.256822232369100
2.89-3.020.3621340.249422352369100
3.02-3.180.41161420.247122412383100
3.18-3.380.27691460.2392210235699
3.38-3.640.26351430.20892201234499
3.64-4.010.24071410.19132251239298
4.01-4.580.21851430.18432180232398
4.59-5.770.22671420.19592250239298
5.77-27.130.18831400.18842325246598

+
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