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- PDB-6l61: Quinolone synthase from Aegle marmelos Correa, Dimer -

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Basic information

Entry
Database: PDB / ID: 6l61
TitleQuinolone synthase from Aegle marmelos Correa, Dimer
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: 1.4 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 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,7712
Polymers85,7712
Non-polymers00
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-8 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.420, 58.560, 59.410
Angle α, β, γ (deg.)115.860, 91.520, 96.640
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.: 2
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.: 813 / 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 Å3/Da / Density % sol: 38.56 %
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: 0.98 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: 1.4→54.85 Å / Num. obs: 129507 / % possible obs: 94.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 1.8
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.045 / Num. unique obs: 4255 / % possible all: 98.2

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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: 1.4→24.964 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.41
RfactorNum. reflection% reflection
Rfree0.2099 6268 5.01 %
Rwork0.1855 --
obs0.1867 125164 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.45 Å2 / Biso mean: 15.0615 Å2 / Biso min: 5.1 Å2
Refinement stepCycle: final / Resolution: 1.4→24.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 0 813 6529
Biso mean---23.98 -
Num. residues----750
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.29581920.29386892
1.4159-1.43260.29632060.2855382593
1.4326-1.450.29772040.2784393394
1.45-1.46840.30811970.2596386494
1.4684-1.48770.25341940.25393693
1.4877-1.50810.25992000.2346387994
1.5081-1.52960.26062160.2405392794
1.5296-1.55250.25682020.2228385094
1.5525-1.57670.24792000.2148396094
1.5767-1.60260.23762100.2071393995
1.6026-1.63020.27172060.2044389695
1.6302-1.65980.23822040.1987393095
1.6598-1.69170.22742300.1963392395
1.6917-1.72630.20681950.1843398295
1.7263-1.76380.20351910.1883394195
1.7638-1.80480.21131940.1808399095
1.8048-1.84990.2061950.1781402396
1.8499-1.89990.21412130.1806397196
1.8999-1.95580.22112050.1844398096
1.9558-2.01890.18932120.1726398996
2.0189-2.0910.2251950.1756399096
2.091-2.17470.18182410.17399197
2.1747-2.27360.19772290.1713398897
2.2736-2.39340.21872350.185399297
2.3934-2.54320.22852150.1848404497
2.5432-2.73940.21181980.1844405498
2.7394-3.01460.19222410.1783401498
3.0146-3.44990.19972200.1682408698
3.4499-4.34270.17222050.1539404998
4.3427-5.40.16722230.1657408298

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