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- PDB-3fk5: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II... -

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Basic information

Entry
Database: PDB / ID: 3fk5
TitleCrystal structure of 3-oxoacyl-(acyl carrier protein) synthase III, FabH (Xoo4209) from Xanthomonas oryzae pv. oryzae KACC10331
Components3-oxoacyl-synthase III
KeywordsTRANSFERASE / Bacterial blight / Xoo4209 / FabH / Xanthomonas oryzae pv. oryzae KACC10331 / Cytoplasm / Multifunctional enzyme
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-synthase III
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNatarajan, S. / Huynh, K.-H. / Kang, L.W.
CitationJournal: To be Published
Title: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III, FabH (Xoo4209) from Xanthomonas oryzae pv. oryzae KACC10331
Authors: Natarajan, S. / Huynh, K.-H. / Kang, L.W.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-synthase III


Theoretical massNumber of molelcules
Total (without water)36,4941
Polymers36,4941
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3-oxoacyl-synthase III

A: 3-oxoacyl-synthase III


Theoretical massNumber of molelcules
Total (without water)72,9882
Polymers72,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4610 Å2
ΔGint-11 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.750, 79.450, 62.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 3-oxoacyl-synthase III / 3-oxoacyl-(acyl carrier protein) synthase III (KASIII)


Mass: 36493.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / Gene: fabH, XOO4209 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5GV10, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M HEPES pH 7.2, 30% PEG 6000, 5% 2-methyl-2, 4-pentanediol, 3% D-galactose , VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→29 Å / Num. all: 21786 / Num. obs: 20632 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.05→2.12 Å / % possible all: 81.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNJ

1hnj


Resolution: 2.05→29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.885 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23692 1111 5.1 %RANDOM
Rwork0.17417 ---
all0.17722 21786 --
obs0.17722 20632 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 245 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222595
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9673517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85923.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53315449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9691520
X-RAY DIFFRACTIONr_chiral_restr0.1430.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211925
X-RAY DIFFRACTIONr_mcbond_it1.1511.51670
X-RAY DIFFRACTIONr_mcangle_it1.99822676
X-RAY DIFFRACTIONr_scbond_it3.3783925
X-RAY DIFFRACTIONr_scangle_it5.314.5841
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 57 -
Rwork0.18 1184 -
obs--100 %

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