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- PDB-7zmc: Ketosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11 -

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Basic information

Entry
Database: PDB / ID: 7zmc
TitleKetosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11
ComponentsPutative polyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / Ketosynthase / polyketide synthase / thiolase fold / Claisen Condensation
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / RhiE-like, KS-MAT linker domain / : / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch ...: / RhiE-like, KS-MAT linker domain / : / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / : / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis NBRC 100599 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative polyketide synthase
B: Putative polyketide synthase


Theoretical massNumber of molelcules
Total (without water)140,1442
Polymers140,1442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-18 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.560, 191.790, 293.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1590 through 2035 or resid 2038 through 2198))
d_2ens_1(chain "B" and (resid 1590 through 1626 or resid 1651 through 1796 or resid 1827 through 2198))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPROA1 - 369
d_12ens_1SERLEUA372 - 532
d_21ens_1ALAPROB2 - 38
d_22ens_1GLYILEB44 - 166
d_23ens_1VALLEUB169 - 538

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Components

#1: Protein Putative polyketide synthase


Mass: 70072.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis NBRC 100599 (bacteria)
Strain: 47 / JCM 6285 / NBRC 100599 / Gene: BBR47_39880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0ZGQ6

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 ul drops of 4 mg ml-1 protein in buffer (20 mM Hepes KOH pH 8.0, 250 mM NaCl, 5 % v/v glycerol, 5 mM DTT) supplemented by 10 mM MgSO4 with 0.15 ul of reservoir solution (0.2 M (NH4)2SO4, ...Details: 0.2 ul drops of 4 mg ml-1 protein in buffer (20 mM Hepes KOH pH 8.0, 250 mM NaCl, 5 % v/v glycerol, 5 mM DTT) supplemented by 10 mM MgSO4 with 0.15 ul of reservoir solution (0.2 M (NH4)2SO4, 0.1 M Na3 citrate pH 5.22, 8 % w/v PEG 3350)

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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: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.97 Å / Num. obs: 38108 / % possible obs: 99.55 % / Redundancy: 13.61 % / Biso Wilson estimate: 105.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.44
Reflection shellResolution: 3.1→3.28 Å / Redundancy: 0.53 % / Num. unique obs: 3437 / CC1/2: 0.419 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z37

4z37


Resolution: 3.1→48.97 Å / SU ML: 0.5529 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.2566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2885 1902 4.99 %
Rwork0.2629 36206 -
obs0.2642 38108 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8379 0 0 0 8379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00338552
X-RAY DIFFRACTIONf_angle_d0.673911573
X-RAY DIFFRACTIONf_chiral_restr0.04641274
X-RAY DIFFRACTIONf_plane_restr0.00491505
X-RAY DIFFRACTIONf_dihedral_angle_d15.01063153
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.3082431265 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.5251280.4832495X-RAY DIFFRACTION97.84
3.18-3.260.44121320.42952509X-RAY DIFFRACTION99.17
3.26-3.360.38541360.39952571X-RAY DIFFRACTION99.41
3.36-3.470.37341330.35872545X-RAY DIFFRACTION99.55
3.47-3.590.37271350.36482553X-RAY DIFFRACTION99.81
3.59-3.740.32571340.35312573X-RAY DIFFRACTION99.45
3.74-3.910.32131350.30362582X-RAY DIFFRACTION99.67
3.91-4.110.31941360.27332579X-RAY DIFFRACTION99.85
4.11-4.370.27081350.24442567X-RAY DIFFRACTION99.96
4.37-4.710.23221380.22062604X-RAY DIFFRACTION99.78
4.71-5.180.25651360.22712596X-RAY DIFFRACTION99.93
5.18-5.930.30581380.24182610X-RAY DIFFRACTION100
5.93-7.460.25151400.24552665X-RAY DIFFRACTION99.96
7.46-48.970.25051460.21172757X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: -31.2516773599 Å / Origin y: -16.3406511113 Å / Origin z: 37.0372630502 Å
111213212223313233
T0.784542253943 Å20.10672065079 Å2-0.0401012823523 Å2-0.927112179677 Å2-0.0282872110998 Å2--0.864936559083 Å2
L0.526420622645 °20.0600987270763 °2-0.0581231884829 °2-1.81821691742 °2-0.799474347385 °2--1.5835549181 °2
S-0.0183353041469 Å °-0.14383880318 Å °-0.0434861563585 Å °0.0484823740013 Å °-0.0754350128269 Å °-0.0731296334618 Å °-0.224959036959 Å °0.228599831714 Å °0.104701434676 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection details: all

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA - B1590 - 21981 - 539
2B1589 - 2199

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