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- PDB-6l73: Quinolone synthase (AmQNS) from Aegle marmelos Correa -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6l73
TitleQuinolone synthase (AmQNS) from Aegle marmelos Correa
ComponentsType III polyketide synthase
KeywordsPLANT PROTEIN / Quinolone synthase / type III PKS
Function / homology
Function and homology information


acridone synthase activity / polyketide biosynthetic process / 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: 2 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, Dimer
Authors: Mallika, V. / Abhinav, K.V. / Soniya, E.V.
History
DepositionOct 30, 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
Water22,1401229
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 area4970 Å2
ΔGint-9 kcal/mol
Surface area26020 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 area4960 Å2
ΔGint-10 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.320, 59.760, 104.510
Angle α, β, γ (deg.)90.040, 96.860, 92.550
Int Tables number1
Space group name H-MP1

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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.: 1229 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5 / Details: 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: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→39.278 Å / Num. obs: 89712 / % possible obs: 97.47 % / Redundancy: 4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.047 / Num. unique obs: 2903

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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: 2→39.247 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.2142 4296 5.01 %
Rwork0.1588 --
obs0.1616 85830 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.47 Å2 / Biso mean: 17.6238 Å2 / Biso min: 4.17 Å2
Refinement stepCycle: final / Resolution: 2→39.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11400 0 0 1229 12629
Biso mean---23.66 -
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 (%)
2-2.02270.27711670.2132268697
2.0227-2.04650.27741300.2085260796
2.0465-2.07150.2861380.2003276196
2.0715-2.09770.25581650.1931265297
2.0977-2.12530.28581240.1896272097
2.1253-2.15440.25491150.1846270697
2.1544-2.18520.22171130.1665276497
2.1852-2.21780.24481200.1675270097
2.2178-2.25250.22341360.1664270697
2.2525-2.28940.24971490.169270797
2.2894-2.32890.24021540.1655269297
2.3289-2.37120.23271390.1708275097
2.3712-2.41680.21511600.1669265998
2.4168-2.46610.24921670.1701273397
2.4661-2.51970.24861220.1711268697
2.5197-2.57830.23761480.1677274497
2.5783-2.64280.23731630.1648266597
2.6428-2.71420.22471500.1675277298
2.7142-2.79410.1971330.1677267898
2.7941-2.88430.24391600.1645272198
2.8843-2.98730.21641660.157272598
2.9873-3.10690.21721260.159272498
3.1069-3.24820.22141480.158274498
3.2482-3.41940.18921360.1522275198
3.4194-3.63350.22041280.1412276198
3.6335-3.91380.18051420.1369274498
3.9138-4.30720.15371410.1278274798
4.3072-4.92940.17071270.1208278599
4.9294-6.20660.17531590.1555271099
6.2066-90.16061700.1461273499

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