[English] 日本語
Yorodumi
- PDB-7zmf: Dehydratase domain of module 3 from Brevibacillus Brevis orphan BGC11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zmf
TitleDehydratase domain of module 3 from Brevibacillus Brevis orphan BGC11
ComponentsPutative polyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / Dehydratase / polyketide synthase / Double hot dog fold
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH ...: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis NBRC 100599 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsTittes, Y.U. / Herbst, D.A. / Jakob, R.P. / Maier, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation179323, 159696, 177084 Switzerland
CitationJournal: Sci Adv / Year: 2022
Title: The structure of a polyketide synthase bimodule core.
Authors: Yves U Tittes / Dominik A Herbst / Solène F X Martin / Hugo Munoz-Hernandez / Roman P Jakob / Timm Maier /
Abstract: Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile ...Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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: Putative polyketide synthase
B: Putative polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9965
Polymers66,8562
Non-polymers1413
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-21 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.380, 197.360, 39.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11B-1617-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1139 through 1205 or resid 1209 through 1250 or resid 1255 through 1430))
d_2ens_1(chain "B" and (resid 1139 through 1358 or resid 1365 through 1392 or resid 1401 through 1430))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLEUA1 - 61
d_12ens_1ARGGLNA65 - 106
d_13ens_1THRVALA111 - 272
d_21ens_1GLYMETD1 - 207
d_22ens_1SERARGD214 - 241
d_23ens_1VALVALD250 - 279

-
Components

#1: Protein Putative polyketide synthase


Mass: 33427.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis NBRC 100599 (bacteria)
Gene: BBR47_39880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0ZGQ6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 ul drops of 3.9 mg ml-1 protein in buffer( 20 mM Hepes KOH pH 8.0, 250 mM NaCl, 5 % v/v glycerol, 5 mM DTT) with 0.2 ul of reservoir solution (20 % w/v PEG 500 MME; 10% PEG 20000, 0.1 M ...Details: 0.2 ul drops of 3.9 mg ml-1 protein in buffer( 20 mM Hepes KOH pH 8.0, 250 mM NaCl, 5 % v/v glycerol, 5 mM DTT) with 0.2 ul of reservoir solution (20 % w/v PEG 500 MME; 10% PEG 20000, 0.1 M Tris;BICINE pH 8.5, 0.06 M MgCl hexahydrate, 0.06 M CaCl dihydrate)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→48.68 Å / Num. obs: 28971 / % possible obs: 99.02 % / Redundancy: 13.39 % / Biso Wilson estimate: 44.38 Å2 / CC1/2: 0.999 / Rsym value: 0.1468 / Net I/σ(I): 14.42
Reflection shellResolution: 2.21→2.26 Å / Num. unique obs: 2086 / CC1/2: 0.67

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hqw

5hqw


Resolution: 2.21→48.68 Å / SU ML: 0.304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 1999 6.9 %
Rwork0.2235 26952 -
obs0.2251 28951 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.84 Å2
Refinement stepCycle: LAST / Resolution: 2.21→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 8 78 4366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054365
X-RAY DIFFRACTIONf_angle_d0.5985895
X-RAY DIFFRACTIONf_chiral_restr0.0472663
X-RAY DIFFRACTIONf_plane_restr0.0043767
X-RAY DIFFRACTIONf_dihedral_angle_d12.38351607
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.63740857784 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.260.32811390.3231868X-RAY DIFFRACTION98.09
2.26-2.320.34531400.31361901X-RAY DIFFRACTION99.17
2.32-2.390.38021390.30631868X-RAY DIFFRACTION99.75
2.39-2.470.31431430.28881937X-RAY DIFFRACTION99.38
2.47-2.560.28591370.28361842X-RAY DIFFRACTION97.2
2.56-2.660.33431400.29441893X-RAY DIFFRACTION97.88
2.66-2.780.33861420.28681916X-RAY DIFFRACTION99.76
2.78-2.930.30121430.26411915X-RAY DIFFRACTION99.9
2.93-3.110.31821420.25181923X-RAY DIFFRACTION99.85
3.11-3.350.28881440.24911940X-RAY DIFFRACTION99.38
3.35-3.690.23511430.211919X-RAY DIFFRACTION98.52
3.69-4.220.20061430.18811939X-RAY DIFFRACTION98.35
4.22-5.310.17051490.15711997X-RAY DIFFRACTION99.72
5.32-48.680.22171550.21212094X-RAY DIFFRACTION98.25
Refinement TLS params.Method: refined / Origin x: 15.8394365294 Å / Origin y: 22.8248612221 Å / Origin z: 0.101442614505 Å
111213212223313233
T0.2945684319 Å20.0419877053602 Å20.00159361182663 Å2-0.377955614569 Å20.0137008903355 Å2--0.246957508587 Å2
L0.371921310733 °2-0.280073476585 °2-0.22622435614 °2-3.48770906296 °21.19460055686 °2--0.851076033165 °2
S-0.0552985480323 Å °-0.0720517983888 Å °0.00964917289829 Å °0.174790372945 Å °-0.000935765627085 Å °0.16788131742 Å °0.183878336026 Å °0.0566514702 Å °0.0504275089432 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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