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- PDB-7zm9: Ketosynthase domain 3 of Brevibacillus Brevis orphan BGC11 -

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Basic information

Entry
Database: PDB / ID: 7zm9
TitleKetosynthase domain 3 of Brevibacillus Brevis orphan BGC11
ComponentsPutative polyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / Ketosynthase / polyketide synthase / Claisen condensation / thiolase 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
DI(HYDROXYETHYL)ETHER / Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis NBRC 100599 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0498
Polymers67,3481
Non-polymers7017
Water9,332518
1
A: Putative polyketide synthase
hetero molecules

A: Putative polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,09716
Polymers134,6952
Non-polymers1,40214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7970 Å2
ΔGint23 kcal/mol
Surface area44020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.780, 92.690, 99.270
Angle α, β, γ (deg.)90.000, 92.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative polyketide synthase


Mass: 67347.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSD in strucutre is an oxidized CYS, and therefore not a sequence missmatch
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
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 ul drop of 12 mg/ml 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 (1 % w/v PEG MME 2k, 1 M Na succinate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→60.483 Å / Num. obs: 145063 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.42 Å2 / Rsym value: 0.048 / Net I/σ(I): 16.6
Reflection shellResolution: 1.62→1.66 Å / Mean I/σ(I) obs: 1.01 / Num. unique obs: 10662 / CC1/2: 0.625 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z37

4z37


Resolution: 1.62→60.483 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 2000 1.38 %
Rwork0.1521 143021 -
obs0.1524 145021 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.05 Å2 / Biso mean: 58.7989 Å2 / Biso min: 21.94 Å2
Refinement stepCycle: final / Resolution: 1.62→60.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 110 519 5281
Biso mean--87.14 55.82 -
Num. residues----596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.62-1.66050.40141420.38081015599
1.6605-1.70540.34381430.332310172100
1.7054-1.75560.31341410.28651011399
1.7556-1.81220.30411420.247410172100
1.8122-1.8770.22631430.217810177100
1.877-1.95220.20021420.195310156100
1.9522-2.0410.16411420.157710203100
2.041-2.14860.15761430.145610231100
2.1486-2.28320.16291430.139210172100
2.2832-2.45950.14921430.132810268100
2.4595-2.7070.16061440.136910248100
2.707-3.09880.17911430.152210268100
3.0988-3.9040.15941440.135110278100
3.904-60.4830.13281450.133510408100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0555-0.65290.28222.36160.6621.2120.05610.13280.4652-0.2455-0.0604-0.4018-0.13030.1891-0.01860.3203-0.00650.07230.35050.10820.539918.958241.950941.238
21.4995-0.16920.09391.67490.14881.13130.03870.060.6736-0.173-0.0592-0.2825-0.30230.03710.06750.3643-0.00180.05460.31390.11020.55269.623552.328540.7536
31.7604-0.24080.04441.6249-0.21790.86990.0583-0.06230.24450.0224-0.0776-0.32850.020.0830.02080.24360.0002-0.00720.24980.01770.278911.123734.94649.3975
41.3428-0.0634-0.12323.03920.77032.51390.0776-0.19060.24570.1333-0.0393-0.9882-0.05760.44270.01860.2721-0.0004-0.10380.46030.03460.715230.491432.599955.4306
52.7877-0.8105-0.23122.76420.24151.4260.00030.1845-0.4363-0.1245-0.2327-0.26460.31240.19970.04140.29820.06130.02870.30340.03980.413519.978319.96147.3595
61.4669-0.7075-0.22051.64711.34141.8704-0.05460.22030.1928-0.16520.1208-0.41610.00540.51180.00050.67760.07540.24180.68910.19630.367319.869234.956916.8712
71.01780.0778-0.05360.55360.26581.2676-0.07310.66780.203-0.51470.0313-0.48260.06440.43760.09180.84020.09770.29380.87710.16140.386519.894634.309713.2319
83.85430.14720.54672.30170.10542.46420.09760.5052-0.1006-0.3927-0.01120.48850.2663-0.33690.01271.10380.07820.10850.99130.0690.42783.555828.40154.6011
91.54210.08310.3510.88280.16551.7741-0.03920.5620.0792-0.41020.07850.0690.25110.18720.00020.58120.02390.14540.55790.14440.35029.884434.832322.6069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 535 through 578 )A535 - 578
2X-RAY DIFFRACTION2chain 'A' and (resid 579 through 640 )A579 - 640
3X-RAY DIFFRACTION3chain 'A' and (resid 641 through 888 )A641 - 888
4X-RAY DIFFRACTION4chain 'A' and (resid 889 through 923 )A889 - 923
5X-RAY DIFFRACTION5chain 'A' and (resid 924 through 965 )A924 - 965
6X-RAY DIFFRACTION6chain 'A' and (resid 966 through 1000 )A966 - 1000
7X-RAY DIFFRACTION7chain 'A' and (resid 1001 through 1057 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1058 through 1096 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1097 through 1130 )A0

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