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- PDB-5o15: Crystal structure of bifunctional dehydratase-cyclase domain in a... -

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Basic information

Entry
Database: PDB / ID: 5o15
TitleCrystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis
ComponentsAmbC
KeywordsLYASE / biocatalysis / cyclases / dehydratases / heterocycles / polyketides / double hotdog fold
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase / 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 ...Polyketide synthase dehydratase / 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 / Thiol Ester Dehydrase; Chain A / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.174 Å
AuthorsSung, K.H. / Berkhan, G. / Hollmann, T. / Wagner, L. / Hahn, F. / Blankenfeldt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationHA 5841/2-1 Germany
European Union293430
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Insights into the Dual Activity of a Bifunctional Dehydratase-Cyclase Domain.
Authors: Sung, K.H. / Berkhan, G. / Hollmann, T. / Wagner, L. / Blankenfeldt, W. / Hahn, F.
History
DepositionMay 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmbC
B: AmbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3663
Polymers64,2742
Non-polymers921
Water13,223734
1
A: AmbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2292
Polymers32,1371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AmbC


Theoretical massNumber of molelcules
Total (without water)32,1371
Polymers32,1371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.841, 91.495, 143.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AmbC


Mass: 32137.109 Da / Num. of mol.: 2
Fragment: bifunctional dehydratase-cyclase domain, UNP residues 918-1228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: ambC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: UniProt: A1YBQ4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.174→91.495 Å / Num. obs: 193120 / % possible obs: 97.7 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.018 / Rrim(I) all: 0.067 / Net I/σ(I): 17.5
Reflection shellResolution: 1.174→1.178 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.204 / Mean I/σ(I) obs: 2 / Num. unique obs: 1855 / CC1/2: 0.701 / Rpim(I) all: 0.353 / Rrim(I) all: 1.256 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
REFMACrefinement
autoPROCdata reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O16

5o16


Resolution: 1.174→40.265 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 16.18
RfactorNum. reflection% reflection
Rfree0.158 9625 4.99 %
Rwork0.1352 --
obs0.1364 192693 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.174→40.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 6 734 4919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014587
X-RAY DIFFRACTIONf_angle_d1.0956339
X-RAY DIFFRACTIONf_dihedral_angle_d14.5391609
X-RAY DIFFRACTIONf_chiral_restr0.091718
X-RAY DIFFRACTIONf_plane_restr0.009851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1738-1.18710.26933210.23595896X-RAY DIFFRACTION95
1.1871-1.20110.2732970.23145925X-RAY DIFFRACTION96
1.2011-1.21580.24212810.21465947X-RAY DIFFRACTION95
1.2158-1.23110.23852990.1925943X-RAY DIFFRACTION96
1.2311-1.24740.22123130.18075997X-RAY DIFFRACTION96
1.2474-1.26440.20493010.17515952X-RAY DIFFRACTION97
1.2644-1.28250.21753060.17666043X-RAY DIFFRACTION96
1.2825-1.30160.19763450.15755823X-RAY DIFFRACTION95
1.3016-1.3220.17033310.14326042X-RAY DIFFRACTION97
1.322-1.34370.17853120.13766001X-RAY DIFFRACTION97
1.3437-1.36680.19533380.13846053X-RAY DIFFRACTION97
1.3668-1.39170.1563110.13176009X-RAY DIFFRACTION97
1.3917-1.41850.15023180.12856111X-RAY DIFFRACTION98
1.4185-1.44740.14523260.1216037X-RAY DIFFRACTION97
1.4474-1.47890.13033380.11386100X-RAY DIFFRACTION99
1.4789-1.51330.14723000.10996138X-RAY DIFFRACTION98
1.5133-1.55110.13733170.10756084X-RAY DIFFRACTION97
1.5511-1.59310.13943170.10535987X-RAY DIFFRACTION96
1.5931-1.640.14862950.10286208X-RAY DIFFRACTION99
1.64-1.69290.13323360.1026153X-RAY DIFFRACTION99
1.6929-1.75340.13863100.10196187X-RAY DIFFRACTION99
1.7534-1.82360.1253050.10596219X-RAY DIFFRACTION99
1.8236-1.90660.13093370.10956210X-RAY DIFFRACTION99
1.9066-2.00710.13563440.11226237X-RAY DIFFRACTION99
2.0071-2.13290.12163490.11376175X-RAY DIFFRACTION98
2.1329-2.29750.15053120.11596085X-RAY DIFFRACTION97
2.2975-2.52870.1463550.12716290X-RAY DIFFRACTION100
2.5287-2.89450.15623200.14136378X-RAY DIFFRACTION100
2.8945-3.64640.16433610.13986389X-RAY DIFFRACTION100
3.6464-40.2890.17683300.16626449X-RAY DIFFRACTION96

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