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- PDB-8z5f: Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in com... -

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Basic information

Entry
Database: PDB / ID: 8z5f
TitleCrystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with decanoyl-ACP from Helicobacter pylori
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / beta-ketoacyl-ACP synthase / FabF / decanoyl-ACP
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / membrane / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / 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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
DECANOIC ACID / Chem-PN7 / 3-oxoacyl-[acyl-carrier-protein] synthase 2 / Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, L. / Huang, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: The beta-Ketoacyl-ACP Synthase FabF Catalyzes Carbon-Carbon Bond Formation in a Bimodal Pattern for Fatty Acid Biosynthesis.
Authors: Huang, Y. / Wang, Y. / Cai, C. / Zhang, L. / Ye, F. / Zhang, L.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

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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 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7838
Polymers105,7224
Non-polymers1,0614
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.312, 153.586, 72.442
Angle α, β, γ (deg.)90.00, 113.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43497.605 Da / Num. of mol.: 2 / Mutation: K336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: CV729_03800, DD764_02895, EC543_05795 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A438WLJ1, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein Acyl carrier protein / ACP


Mass: 9363.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: acpP, acpP_2, AA971_03770, ACM26_04180, ACM37_01955, AEY53_01410, AM496_03540, AM497_00990, AP069_0203010, AV920_0203940, B0X29_03800, B0X45_00570, B0X60_00365, BB384_06970, BB395_06520, BB411_ ...Gene: acpP, acpP_2, AA971_03770, ACM26_04180, ACM37_01955, AEY53_01410, AM496_03540, AM497_00990, AP069_0203010, AV920_0203940, B0X29_03800, B0X45_00570, B0X60_00365, BB384_06970, BB395_06520, BB411_01045, BB413_00115, BB414_01745, BB424_04705, BB425_06615, BB461_04255, BB464_01665, BGL66_01950, BGL69_04330, BGL75_08125, BHU51_05610, BV499_06310, BZK21_01490, BZK27_00480, C2R62_01950, C2R66_01755, C2R85_07050, C2R93_06190, C2R96_08170, C2S01_06755, C2S04_07420, C2S07_01945, C2S19_07900, C2S39_07050, C2S42_07730, C2S44_03705, CGC32_03355, CHC155_06320, CV726_04705, CV727_03490, CV728_03285, CV729_03805, CV730_03675, D2C82_03205, D2C84_02485, D8X56_02965, DD750_02355, DD779_02830, DDP35_03120, DDP37_03425, DDP42_02985, DDP44_02790, DDP47_01920, DDP49_02455, DDP57_02830, EC503_03190, EC505_03755, EC511_02300, EC517_03570, EC518_00005, EC525_03720, EC532_06155, EC533_02570, EC547_02800, EC550_02360, EC556_02625, EC558_03510, EC565_04600, EC572_05195, EC585_03955, EC589_03210, EC590_01945, ECC07_01920, ECC12_02075, ECC24_01300, ECC33_03205, ECC34_03320, ECC35_03300, ECC38_04160, ECC40_02350, ECC41_02110, ECC43_03930, ECC49_04200, EDA74_03725, EDB75_01310, EDC13_02400, EGV97_06255, EGW01_07925, EPC79_07230, EPC80_01035, F7187_05530, F7189_04775, F7197_04985, F7198_04545, F7213_06745, F7220_05045, F7229_06460, HPF17_0447, HPF209_0807, HPF210_0847, HPF72_0568, HPK21_01210, HPMKM5_0823, HPPMSS1_c00678, HPY1846_06495
Production host: Escherichia coli (E. coli) / References: UniProt: Q5EDC8
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H20O2 / Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-PN7 / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 358.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H23N2O7PS / Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH6.5, 15% w/v PEG 4000 and 20% w/v glycerin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.95→33.27 Å / Num. obs: 80031 / % possible obs: 95.9 % / Redundancy: 5.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.063 / Rrim(I) all: 0.158 / Χ2: 0.82 / Net I/σ(I): 5.7 / Num. measured all: 471141
Reflection shellResolution: 1.95→2 Å / % possible obs: 71.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.572 / Num. measured all: 15640 / Num. unique obs: 4390 / CC1/2: 0.786 / Rpim(I) all: 0.33 / Rrim(I) all: 0.666 / Χ2: 0.66 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→33.27 Å / Cross valid method: FREE R-VALUE / σ(F): 57.55 / Phase error: 61.35 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2776 4215 5.27 %
Rwork0.2722 --
obs0.4238 79995 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7378 0 0 310 7688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097503
X-RAY DIFFRACTIONf_angle_d1.16210122
X-RAY DIFFRACTIONf_dihedral_angle_d17.9852790
X-RAY DIFFRACTIONf_chiral_restr0.0731135
X-RAY DIFFRACTIONf_plane_restr0.0111339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.41181570.42652710X-RAY DIFFRACTION66
1.98-2.020.45121610.4353021X-RAY DIFFRACTION72
2.02-2.060.44781960.44383300X-RAY DIFFRACTION79
2.06-2.10.46152210.44713583X-RAY DIFFRACTION86
2.1-2.150.48292300.46143827X-RAY DIFFRACTION92
2.15-2.20.51312020.47073962X-RAY DIFFRACTION94
2.2-2.250.47261820.49143917X-RAY DIFFRACTION96
2.25-2.310.48761940.50064002X-RAY DIFFRACTION95
2.31-2.380.50362030.48383951X-RAY DIFFRACTION95
2.38-2.460.49222300.51643930X-RAY DIFFRACTION94
2.46-2.540.52022290.50053944X-RAY DIFFRACTION94
2.54-2.650.5192090.49553965X-RAY DIFFRACTION95
2.65-2.770.46421830.48813984X-RAY DIFFRACTION96
2.77-2.910.45192450.4683925X-RAY DIFFRACTION94
2.91-3.090.46541980.45063993X-RAY DIFFRACTION95
3.09-3.330.41272080.40353954X-RAY DIFFRACTION95
3.33-3.670.43682210.39583941X-RAY DIFFRACTION95
3.67-4.20.40332170.38963968X-RAY DIFFRACTION95
4.2-5.290.35011970.364009X-RAY DIFFRACTION95
5.29-33.270.36421890.36844037X-RAY DIFFRACTION95

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