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- PDB-6j1m: Anisodus acutangulus type III polyketide sythase AaPKS2 in comple... -

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Basic information

Entry
Database: PDB / ID: 6j1m
TitleAnisodus acutangulus type III polyketide sythase AaPKS2 in complex with 4-carboxy-3-oxobutanoyl covalent to C166
ComponentsA. acutangulus PKS2
KeywordsBIOSYNTHETIC PROTEIN / Anisodus acutangulus / type III polyketide sythase / tropane alkaloids biosythesis
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / 3-oxopentanedioic acid
Function and homology information
Biological speciesAnisodus acutangulus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsFang, C.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Nat Commun / Year: 2019
Title: Tropane alkaloids biosynthesis involves an unusual type III polyketide synthase and non-enzymatic condensation.
Authors: Huang, J.P. / Fang, C. / Ma, X. / Wang, L. / Yang, J. / Luo, J. / Yan, Y. / Zhang, Y. / Huang, S.X.
History
DepositionDec 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A. acutangulus PKS2
B: A. acutangulus PKS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9948
Polymers93,4542
Non-polymers5406
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint3 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.144, 108.144, 191.075
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

21B-756-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 16 and (name N or name...
21(chain B and (resid 16 through 52 or (resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 16 and (name N or name...AA1652
12LYSLYSILEILE(chain A and ((resid 16 and (name N or name...AA11 - 39147 - 427
13LYSLYSILEILE(chain A and ((resid 16 and (name N or name...AA11 - 39147 - 427
14LYSLYSILEILE(chain A and ((resid 16 and (name N or name...AA11 - 39147 - 427
15LYSLYSILEILE(chain A and ((resid 16 and (name N or name...AA11 - 39147 - 427
21GLUGLUVALVAL(chain B and (resid 16 through 52 or (resid 53...BB16 - 5252 - 88
22ASPASPASPASP(chain B and (resid 16 through 52 or (resid 53...BB5389
23GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427
24GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427
25GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427
26GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427
27GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427
28GLUGLUILEILE(chain B and (resid 16 through 52 or (resid 53...BB16 - 39152 - 427

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Components

#1: Protein A. acutangulus PKS2


Mass: 46726.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anisodus acutangulus (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-6JN / 3-oxopentanedioic acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1% tryptone, 0.05M HEPES 7.0, 20% PEG3350, 0.001M sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 87808 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 11 % / Biso Wilson estimate: 41.89 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.032 / Rrim(I) all: 0.107 / Rsym value: 0.104 / Χ2: 0.931 / Net I/σ(I): 24.892
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.1 % / Num. unique obs: 4331 / CC1/2: 0.922 / Rpim(I) all: 0.293 / Rrim(I) all: 0.972 / Χ2: 0.922 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CML

1cml


Resolution: 2.001→47.058 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2004 2.36 %
Rwork0.1805 83053 -
obs0.1808 85057 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 28.2921 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: final / Resolution: 2.001→47.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5789 0 34 627 6450
Biso mean--40.04 37.2 -
Num. residues----757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3527X-RAY DIFFRACTION3.999TORSIONAL
12B3527X-RAY DIFFRACTION3.999TORSIONAL
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 (%)
2.0006-2.05070.31871010.2754127422868
2.0507-2.10610.26121310.25745409554089
2.1061-2.16810.26251410.23145959610098
2.1681-2.2380.24541500.225660416191100
2.238-2.3180.24051410.21360466187100
2.318-2.41080.23241470.201361126259100
2.4108-2.52060.18981450.198760546199100
2.5206-2.65340.22461430.18960936236100
2.6534-2.81970.23061490.188461216270100
2.8197-3.03730.2191480.187561146262100
3.0373-3.34290.181510.177261446295100
3.3429-3.82650.15831510.159661636314100
3.8265-4.82020.15511480.141362346382100
4.8202-47.07080.16141580.160164366594100

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