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- PDB-8z5e: Crystal structure of beta-ketoacyl-ACP synthase FabF K336A in com... -

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Basic information

Entry
Database: PDB / ID: 8z5e
TitleCrystal structure of beta-ketoacyl-ACP synthase FabF K336A in complex with octanoyl-ACP from Helicobacter pylori
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / beta-ketoacyl-ACP synthase / FabF / octanoyl-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
OCTANOIC ACID (CAPRYLIC 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: 2.2 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 9, 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

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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: 3-oxoacyl-[acyl-carrier-protein] synthase 2
E: 3-oxoacyl-[acyl-carrier-protein] synthase 2
F: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,35912
Polymers193,0666
Non-polymers1,2946
Water14,394799
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1806
Polymers96,5333
Non-polymers6473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-49 kcal/mol
Surface area28720 Å2
MethodPISA
2
D: 3-oxoacyl-[acyl-carrier-protein] synthase 2
E: 3-oxoacyl-[acyl-carrier-protein] synthase 2
F: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1806
Polymers96,5333
Non-polymers6473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-49 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.857, 115.691, 127.933
Angle α, β, γ (deg.)90.00, 89.94, 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: 43584.684 Da / Num. of mol.: 4 / 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-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H16O2 / 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.: 799 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole, pH6.5, and 25% w/v PEG 20000

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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: 2.2→50 Å / Num. obs: 86343 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Χ2: 0.912 / Net I/σ(I): 7.7 / Num. measured all: 588547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.90.40285800.9310.9820.1790.4410.98799.9
2.28-2.376.90.34985730.9640.9910.1430.3780.96100
2.37-2.486.80.27586040.9760.9940.1130.2970.936100
2.48-2.6170.21986110.9810.9950.0890.2360.935100
2.61-2.776.80.16686170.9860.9960.0680.1790.907100
2.77-2.996.90.12786410.990.9970.0520.1380.865100
2.99-3.2970.10186230.9910.9980.0410.1090.799100
3.29-3.766.80.08386340.9910.9980.0340.090.779100
3.76-4.7470.07486820.9920.9980.030.080.76699.9
4.74-506.90.08487780.9860.9960.0340.0911.20499.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.52 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 4088 4.91 %
Rwork0.1643 --
obs0.1667 83197 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13479 0 0 799 14278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813714
X-RAY DIFFRACTIONf_angle_d0.97918490
X-RAY DIFFRACTIONf_dihedral_angle_d17.3235094
X-RAY DIFFRACTIONf_chiral_restr0.0622064
X-RAY DIFFRACTIONf_plane_restr0.0072449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.2717940.1941862X-RAY DIFFRACTION66
2.23-2.250.2483970.19152200X-RAY DIFFRACTION77
2.25-2.280.2891120.19952289X-RAY DIFFRACTION81
2.28-2.310.28841290.19642456X-RAY DIFFRACTION87
2.31-2.340.23821280.18762580X-RAY DIFFRACTION91
2.34-2.380.27061170.18532683X-RAY DIFFRACTION94
2.38-2.410.24961480.18632692X-RAY DIFFRACTION96
2.41-2.450.2321450.18782818X-RAY DIFFRACTION98
2.45-2.490.22521680.16762757X-RAY DIFFRACTION99
2.49-2.530.2391410.16672830X-RAY DIFFRACTION99
2.53-2.580.22251280.16672844X-RAY DIFFRACTION100
2.58-2.630.21411440.17362801X-RAY DIFFRACTION100
2.63-2.680.24641370.1652850X-RAY DIFFRACTION100
2.68-2.740.21461630.17862793X-RAY DIFFRACTION100
2.74-2.810.22081400.17782883X-RAY DIFFRACTION100
2.81-2.880.23251400.17182788X-RAY DIFFRACTION100
2.88-2.950.21111760.17542847X-RAY DIFFRACTION100
2.95-3.040.21651540.16892805X-RAY DIFFRACTION100
3.04-3.140.23681500.17462818X-RAY DIFFRACTION100
3.14-3.250.23581410.16792867X-RAY DIFFRACTION100
3.25-3.380.20371530.1742832X-RAY DIFFRACTION100
3.38-3.540.21261740.16372795X-RAY DIFFRACTION100
3.54-3.720.19691380.15662871X-RAY DIFFRACTION100
3.72-3.950.20091170.1492880X-RAY DIFFRACTION100
3.95-4.260.16531280.13792874X-RAY DIFFRACTION100
4.26-4.690.18021630.12962806X-RAY DIFFRACTION100
4.69-5.360.18691310.15292884X-RAY DIFFRACTION100
5.36-6.750.20271620.17372840X-RAY DIFFRACTION100
6.75-34.520.20251700.16262864X-RAY DIFFRACTION99

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