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- PDB-5by7: AbyA1 - tetronic acid condensing enzyme -

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Basic information

Entry
Database: PDB / ID: 5by7
TitleAbyA1 - tetronic acid condensing enzyme
Components3-oxoacyl-ACP synthase III
KeywordsTRANSFERASE / Tetronate / Polyketide / Natural Product / Condensation
Function / homology
Function and homology information


secondary metabolite biosynthetic process / 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-ACP synthase III
Similarity search - Component
Biological speciesVerrucosispora maris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsByrne, M.J. / Race, P.R.
CitationJournal: To Be Published
Title: The structure of AbyA1, a tetronic acid condensing enzyme from the Abyssomicin polyketide synthase.
Authors: Byrne, M.J. / Race, P.R.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-ACP synthase III
B: 3-oxoacyl-ACP synthase III
C: 3-oxoacyl-ACP synthase III
D: 3-oxoacyl-ACP synthase III


Theoretical massNumber of molelcules
Total (without water)153,0584
Polymers153,0584
Non-polymers00
Water8,647480
1
A: 3-oxoacyl-ACP synthase III
D: 3-oxoacyl-ACP synthase III


Theoretical massNumber of molelcules
Total (without water)76,5292
Polymers76,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-33 kcal/mol
Surface area22340 Å2
MethodPISA
2
B: 3-oxoacyl-ACP synthase III
C: 3-oxoacyl-ACP synthase III


Theoretical massNumber of molelcules
Total (without water)76,5292
Polymers76,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-33 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.710, 58.690, 128.800
Angle α, β, γ (deg.)90.00, 95.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
3-oxoacyl-ACP synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase III


Mass: 38264.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucosispora maris (strain AB-18-032) (bacteria)
Gene: abyA1, VAB18032_16460 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F4F7F9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryological conditions
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→55.67 Å / Num. obs: 122145 / % possible obs: 100 % / Redundancy: 6.1 % / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.8→55.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.283 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22125 6050 5 %RANDOM
Rwork0.18542 ---
obs0.18717 116115 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20.18 Å2
2--0.54 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9122 0 0 480 9602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199232
X-RAY DIFFRACTIONr_bond_other_d0.0020.028935
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.97712573
X-RAY DIFFRACTIONr_angle_other_deg1.047320300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51451259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38322.632323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.439151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651579
X-RAY DIFFRACTIONr_chiral_restr0.1190.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110629
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021995
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6751.4885069
X-RAY DIFFRACTIONr_mcbond_other1.6751.4885068
X-RAY DIFFRACTIONr_mcangle_it2.4612.2216317
X-RAY DIFFRACTIONr_mcangle_other2.4612.2216318
X-RAY DIFFRACTIONr_scbond_it2.6181.8444163
X-RAY DIFFRACTIONr_scbond_other2.6181.8444164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.962.6086257
X-RAY DIFFRACTIONr_long_range_B_refined5.63513.04510082
X-RAY DIFFRACTIONr_long_range_B_other5.5512.7829848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 464 -
Rwork0.182 8494 -
obs--99.99 %

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