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- PDB-7f28: Crystal structure of a bacterial ketosynthase -

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Basic information

Entry
Database: PDB / ID: 7f28
TitleCrystal structure of a bacterial ketosynthase
Components
  • Ketoacyl_synth_N domain-containing protein
  • Putative 3-oxoacyl-[ACP] synthase FabV
KeywordsLIGASE / ketosynthase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Ketoacyl_synth_N domain-containing protein / Putative 3-oxoacyl-[ACP] synthase FabV
Similarity search - Component
Biological speciesAcinetobacter baumannii NCGM 237 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.877 Å
AuthorsLee, W.C. / Kim, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)MSIP-2019R1H1A2079889 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: Ketoacyl_synth_N domain-containing protein
B: Putative 3-oxoacyl-[ACP] synthase FabV
C: Ketoacyl_synth_N domain-containing protein
D: Putative 3-oxoacyl-[ACP] synthase FabV


Theoretical massNumber of molelcules
Total (without water)131,2074
Polymers131,2074
Non-polymers00
Water7,692427
1
A: Ketoacyl_synth_N domain-containing protein
B: Putative 3-oxoacyl-[ACP] synthase FabV


Theoretical massNumber of molelcules
Total (without water)65,6032
Polymers65,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-41 kcal/mol
Surface area21550 Å2
MethodPISA
2
C: Ketoacyl_synth_N domain-containing protein
D: Putative 3-oxoacyl-[ACP] synthase FabV


Theoretical massNumber of molelcules
Total (without water)65,6032
Polymers65,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-39 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.708, 104.243, 98.179
Angle α, β, γ (deg.)90.000, 98.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ketoacyl_synth_N domain-containing protein


Mass: 22488.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii NCGM 237 (bacteria)
Gene: AB237_2962 / Production host: Acinetobacter baumannii (bacteria) / References: UniProt: A0A0E1PUF7
#2: Protein Putative 3-oxoacyl-[ACP] synthase FabV / ketosynthase


Mass: 43114.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii NCGM 237 (bacteria)
Gene: AB237_2951 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0E1Q0H1, beta-ketoacyl-[acyl-carrier-protein] synthase I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium malonate, 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: 1.877→39.05 Å / Num. obs: 171271 / % possible obs: 98.4 % / Redundancy: 3.684 % / Biso Wilson estimate: 21.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.083 / Χ2: 0.996 / Net I/σ(I): 12.76
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
1.88-1.993.4180.4443.264529214333132510.8960.52392.5
1.99-2.133.7490.2835.545016413462133790.9530.33199.4
2.13-2.33.7530.17984686912542124890.980.20999.6
2.3-2.523.760.12110.854333711567115270.9890.14199.7
2.52-2.813.7630.08214.223914110429104010.9940.09699.7
2.81-3.253.7550.05718.2534626924992210.9970.06699.7
3.25-3.973.7070.03924.728950782778100.9980.04699.8
3.97-5.63.6730.03428.3622261608960600.9980.0499.5
5.6-39.053.4880.03527.6511804344633840.9980.04198.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0F

3u0f


Resolution: 1.877→39.05 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 3896 2.27 %
Rwork0.1904 167375 -
obs0.1913 171271 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.57 Å2 / Biso mean: 24.6394 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 1.877→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 0 427 9393
Biso mean---27.06 -
Num. residues----1181
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8774-1.90030.3652900.334382462
1.9003-1.92440.33061340.2793568993
1.9244-1.94970.29141420.2658608098
1.9497-1.97640.28141340.2465592099
1.9764-2.00460.29861420.2444613499
2.0046-2.03460.29041420.2413607599
2.0346-2.06630.24821400.2349602799
2.0663-2.10020.271420.225607899
2.1002-2.13640.31091390.2118606099
2.1364-2.17530.24571450.2091606499
2.1753-2.21710.23871430.2059605499
2.2171-2.26240.26411430.1959609099
2.2624-2.31160.23461430.19486084100
2.3116-2.36530.2411400.2006606299
2.3653-2.42450.23521420.19986102100
2.4245-2.490.27741450.1943612199
2.49-2.56330.25761430.1989606299
2.5633-2.6460.23111430.20286107100
2.646-2.74050.24361420.19866134100
2.7405-2.85020.23871370.20476070100
2.8502-2.97990.22041430.20456064100
2.9799-3.13690.25441380.20276063100
3.1369-3.33340.25631410.18686100100
3.3334-3.59060.24251400.18096128100
3.5906-3.95160.19951450.15216098100
3.9516-4.52270.16841410.1442610799
4.5227-5.69530.13841360.1499604999
5.6953-39.050.18191410.157592997

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