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- PDB-7f27: Crystal structure of polyketide ketosynthase -

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Basic information

Entry
Database: PDB / ID: 7f27
TitleCrystal structure of polyketide ketosynthase
Components3-oxoacyl-(Acyl-carrier-protein) synthase
KeywordsLIGASE / thiolase fold / ketosynthase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase / 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 / Thiolase-like
Similarity search - Domain/homology
3-oxoacyl-(Acyl-carrier-protein) synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.806 Å
AuthorsKim, Y. / Lee, W.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Rep / Year: 2021
Title: Structural basis of the complementary activity of two ketosynthases in aryl polyene biosynthesis.
Authors: Lee, W.C. / Choi, S. / Jang, A. / Yeon, J. / Hwang, E. / Kim, Y.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
B: 3-oxoacyl-(Acyl-carrier-protein) synthase
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase


Theoretical massNumber of molelcules
Total (without water)174,9914
Polymers174,9914
Non-polymers00
Water13,097727
1
A: 3-oxoacyl-(Acyl-carrier-protein) synthase
B: 3-oxoacyl-(Acyl-carrier-protein) synthase


Theoretical massNumber of molelcules
Total (without water)87,4952
Polymers87,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-53 kcal/mol
Surface area26250 Å2
MethodPISA
2
C: 3-oxoacyl-(Acyl-carrier-protein) synthase
D: 3-oxoacyl-(Acyl-carrier-protein) synthase


Theoretical massNumber of molelcules
Total (without water)87,4952
Polymers87,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-48 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.576, 109.525, 122.902
Angle α, β, γ (deg.)90.000, 97.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-(Acyl-carrier-protein) synthase / polyketide ketosynthase


Mass: 43747.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ACICU) (bacteria)
Gene: ACICU_00534 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U3XWE2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 9.1 / Details: 0.2M sodium phosphate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.806→40.683 Å / Num. obs: 282116 / % possible obs: 97.2 % / Redundancy: 3.577 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.065 / Χ2: 1.052 / Net I/σ(I): 13.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.922.730.4532.085624824287206040.8430.56684.8
1.92-2.053.7120.3114.068441922761227400.9530.36499.9
2.05-2.213.7750.1777.148016721262212350.980.20799.9
2.21-2.423.7680.11810.427381219618195870.9890.13799.8
2.42-2.713.7550.07914.796614817649176180.9940.09399.8
2.71-3.123.7320.05520.745831815658156280.9960.06499.8
3.12-3.823.6780.03728.894858113248132100.9980.04399.7
3.82-5.393.6210.03134.193705910300102350.9980.03799.4
5.39-40.6833.4230.03233.8619172583656010.9970.03896

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KAS

1kas


Resolution: 1.806→40.683 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 3845 1.36 %
Rwork0.1745 278271 -
obs0.1748 282116 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.45 Å2 / Biso mean: 33.3632 Å2 / Biso min: 16.57 Å2
Refinement stepCycle: final / Resolution: 1.806→40.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12197 0 0 727 12924
Biso mean---35.54 -
Num. residues----1628
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8064-1.82920.3193690.337500546
1.8292-1.85330.30251130.2974858079
1.8533-1.87870.33731210.2839901883
1.8787-1.90550.28021350.2616958188
1.9055-1.9340.31741360.25571029594
1.934-1.96420.23951490.23821064797
1.9642-1.99640.21391490.22981059498
1.9964-2.03080.29641420.21641067498
2.0308-2.06770.22651490.21861065998
2.0677-2.10750.22881490.2031067798
2.1075-2.15050.22821480.19771066698
2.1505-2.19730.21521480.1951071098
2.1973-2.24840.24551530.19881075599
2.2484-2.30460.19361520.19231072599
2.3046-2.36690.20051470.19051069599
2.3669-2.43650.22751510.19061072799
2.4365-2.51520.18651450.19061082399
2.5152-2.60510.20521520.18391078199
2.6051-2.70930.23041540.1841073699
2.7093-2.83260.20951480.187510854100
2.8326-2.98190.21671450.177210834100
2.9819-3.16870.17761500.176310769100
3.1687-3.41320.1841490.167710840100
3.4132-3.75650.1521490.15310768100
3.7565-4.29950.16631460.1371079499
4.2995-5.4150.16521500.13111078499
5.415-40.6830.15741460.14391028094

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