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- PDB-6l78: Quinolone synthase (QNS) from Aegle marmelos -

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Basic information

Entry
Database: PDB / ID: 6l78
TitleQuinolone synthase (QNS) from Aegle marmelos
ComponentsType III polyketide synthase
KeywordsPLANT PROTEIN / Quinolone synthase / type III PKS
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / endoplasmic reticulum
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Type III polyketide synthase
Similarity search - Component
Biological speciesAegle marmelos (Bengal quince)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsMallika, V. / Abhinav, K.V. / Soniya, E.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research09/716(0178)/2018-EMR-1 dated 26.04.2018 India
CitationJournal: To Be Published
Title: Quinolone synthase from Aegle marmelos Correa
Authors: Mallika, V. / Abhinav, K.V. / Soniya, E.V.
History
DepositionOct 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III polyketide synthase
B: Type III polyketide synthase
C: Type III polyketide synthase
D: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)171,5424
Polymers171,5424
Non-polymers00
Water24,9511385
1
A: Type III polyketide synthase
B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)85,7712
Polymers85,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-9 kcal/mol
Surface area25670 Å2
MethodPISA
2
C: Type III polyketide synthase
D: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)85,7712
Polymers85,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-9 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.770, 115.770, 85.890
Angle α, β, γ (deg.)90.000, 105.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type III polyketide synthase / Quinolone synthase


Mass: 42885.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aegle marmelos (Bengal quince) / Production host: Escherichia coli (E. coli) / References: UniProt: M1HE54
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5 / Details: 0.1M HEPES (pH-7.5), 0.2M NaCl, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→24.88 Å / Num. obs: 193197 / % possible obs: 91.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 0.86
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.031 / Num. unique obs: 6786 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wd7

3wd7


Resolution: 1.55→24.876 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.222 8966 5.03 %
Rwork0.1844 --
obs0.1863 178404 90.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.28 Å2 / Biso mean: 18.6079 Å2 / Biso min: 5.24 Å2
Refinement stepCycle: final / Resolution: 1.55→24.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11400 0 0 1385 12785
Biso mean---27.25 -
Num. residues----1500
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.56760.24843460.2327616399
1.5676-1.58610.27643260.2384616599
1.5861-1.60540.28953450.2336614499
1.6054-1.62570.27033230.2191611899
1.6257-1.64710.25983340.2137616899
1.6471-1.66970.26543310.2086616799
1.6697-1.69350.25273150.2169621999
1.6935-1.71880.2543280.1983615099
1.7188-1.74560.26552050.1958382061
1.7456-1.77420.24173050.2011625399
1.7742-1.80480.24483160.1928619099
1.8048-1.83760.23623630.193617099
1.8376-1.8730.23583350.1853621099
1.873-1.91120.23422170.189458773
1.9112-1.95270.25751480.1879281664
1.9527-1.99810.20092750.17845180100
1.9981-2.04810.22263450.18026200100
2.0481-2.10340.22871870.1878398863
2.1034-2.16530.21743270.18086212100
2.1653-2.23510.2283270.1766251100
2.2351-2.3150.22351760.18043833100
2.315-2.40760.22453640.18526229100
2.4076-2.5170.22773450.18386231100
2.517-2.64960.23733160.19096254100
2.6496-2.81540.23082670.1956456073
2.8154-3.03240.23233230.18736296100
3.0324-3.3370.20663190.1746299100
3.337-3.81830.1832460.1639471175
3.8183-4.8050.18772570.1522564489
4.805-6.90.19363550.1854621098

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