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- PDB-8z5c: Cystal structure of beta-ketoacyl-ACP synthase FabF from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 8z5c
TitleCystal structure of beta-ketoacyl-ACP synthase FabF from Helicobacter pylori
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsBIOSYNTHETIC PROTEIN / beta-ketoacyl-ACP synthase / FabF
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / 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 / Thiolase-like
Similarity search - Domain/homology
RUBIDIUM ION / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2824
Polymers87,1112
Non-polymers1712
Water13,709761
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-77 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.608, 95.382, 113.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43555.707 Da / Num. of mol.: 2
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: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 48.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH7.5, 25% w/v PEG 4000, and 10 mM Rubidium chloride

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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: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 71612 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.188 / Χ2: 1.017 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.86-1.9312.80.87170580.8550.960.2520.9070.8
1.93-2130.6670610.910.9760.190.6870.846
2-2.0912.80.51670710.9450.9860.1490.5370.916
2.09-2.21120.40571060.9590.990.1210.4230.964
2.21-2.3413.40.32671000.9710.9930.0920.3381.038
2.34-2.5213.40.26671150.9790.9950.0750.2761.064
2.52-2.7812.80.21571520.9830.9960.0620.2241.067
2.78-3.1813.30.17871860.9880.9970.050.1851.113
3.18-4.0113.10.15572370.990.9980.0440.1621.199
4.01-5012.70.14675260.9750.9940.0430.1531.137

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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: 1.85→45.7 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 3529 4.97 %
Rwork0.1577 --
obs0.1595 70989 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 2 761 6823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016240
X-RAY DIFFRACTIONf_angle_d1.2038415
X-RAY DIFFRACTIONf_dihedral_angle_d14.6462313
X-RAY DIFFRACTIONf_chiral_restr0.068934
X-RAY DIFFRACTIONf_plane_restr0.0111118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.25341120.20942122X-RAY DIFFRACTION78
1.87-1.90.26941360.20332613X-RAY DIFFRACTION96
1.9-1.930.25941490.1992585X-RAY DIFFRACTION97
1.93-1.960.24971490.18632678X-RAY DIFFRACTION99
1.96-1.990.19641270.18762693X-RAY DIFFRACTION99
1.99-2.030.23821460.18492670X-RAY DIFFRACTION100
2.03-2.060.22191460.18342690X-RAY DIFFRACTION99
2.06-2.10.25071470.17632698X-RAY DIFFRACTION100
2.1-2.150.26291680.16812679X-RAY DIFFRACTION100
2.15-2.190.22091390.1672717X-RAY DIFFRACTION100
2.19-2.240.18511500.15962677X-RAY DIFFRACTION100
2.24-2.30.20231390.16212708X-RAY DIFFRACTION100
2.3-2.360.2051370.16312725X-RAY DIFFRACTION100
2.36-2.430.21281320.16462728X-RAY DIFFRACTION100
2.43-2.510.19411260.16012745X-RAY DIFFRACTION100
2.51-2.60.21991310.16252725X-RAY DIFFRACTION100
2.6-2.70.20381220.15682757X-RAY DIFFRACTION100
2.7-2.830.19321400.15492722X-RAY DIFFRACTION100
2.83-2.980.19361430.16412762X-RAY DIFFRACTION100
2.98-3.160.18091480.16122730X-RAY DIFFRACTION100
3.16-3.410.20771570.15362753X-RAY DIFFRACTION100
3.41-3.750.17851390.14542752X-RAY DIFFRACTION100
3.75-4.290.15611250.12962810X-RAY DIFFRACTION100
4.29-5.40.14981540.1282805X-RAY DIFFRACTION100
5.41-45.70.1451670.15552916X-RAY DIFFRACTION99

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