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- PDB-9knj: Crystal structure of glycerol-bound full-length PHA synthase (Pha... -

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Basic information

Entry
Database: PDB / ID: 9knj
TitleCrystal structure of glycerol-bound full-length PHA synthase (PhaC) from Aeromonas caviae
ComponentsPHA synthase
KeywordsBIOSYNTHETIC PROTEIN / PHA synthase / full-length PhaC structure / dimer / tunnel / catalytic triad / glycerol / polyhydroxyalkanoate
Function / homologyPoly-beta-hydroxybutyrate polymerase, N-terminal domain / Poly(R)-hydroxyalkanoic acid synthase, class I / : / Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus / poly-hydroxybutyrate biosynthetic process / acyltransferase activity / Alpha/Beta hydrolase fold / cytoplasm / PHA synthase
Function and homology information
Biological speciesAeromonas caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization (NEDO)P20005 Japan
Japan Science and Technology29A1027 Japan
Japan Society for the Promotion of Science (JSPS)21K5028 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Structures of Polyhydroxyalkanoate Synthase PhaC from Aeromonas caviae, Producing Biodegradable Plastics.
Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Matsumoto, K. / Sato, S. / Hakoshima, T.
History
DepositionNov 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHA synthase
B: PHA synthase
C: PHA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,67614
Polymers199,6633
Non-polymers1,01311
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Monomer-dimer equilibrium, gel filtration, Monomer-dimer equilibrium
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.032, 96.071, 143.296
Angle α, β, γ (deg.)90.000, 90.420, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 40 or resid 53...
d_2ens_1(chain "B" and (resid 5 through 77 or resid 105...
d_3ens_1(chain "C" and (resid 5 through 40 or resid 53...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERLEULEUAA5 - 407 - 42
d_12GLNGLNLEULEUAA53 - 7755 - 79
d_13GLNGLNLEULEUAA105 - 166107 - 168
d_14ASPASPASNASNAA171 - 194173 - 196
d_15PHEPHEARGARGAA203 - 553205 - 555
d_16GLUGLUPROPROAA558 - 583560 - 585
d_17GOLGOLGOLGOLAF603
d_21SERSERLEULEUBB5 - 777 - 79
d_22GLNGLNLEULEUBB105 - 166107 - 168
d_23ASPASPASNASNBB171 - 194173 - 196
d_24PHEPHEARGARGBB203 - 553205 - 555
d_25GLUGLUPROPROBB558 - 583560 - 585
d_26GOLGOLGOLGOLBK603
d_31SERSERLEULEUCC5 - 407 - 42
d_32GLNGLNLEULEUCC53 - 7755 - 79
d_33GLNGLNASNASNCC105 - 194107 - 196
d_34PHEPHEPROPROCC203 - 583205 - 585
d_35GOLGOLGOLGOLCM601

NCS oper:
IDCodeMatrixVector
1given(0.456425170661, -0.889246047369, -0.0302907712805), (-0.887348698739, -0.452417880868, -0.0890525009047), (0.0654854978853, 0.0675242794028, -0.995566231477)5.95315826582, -76.4060249109, 101.288550773
2given(-0.446619192675, -0.893308726761, 0.050307210492), (0.893787775271, -0.442874282119, 0.0707515583807), (-0.0409232148014, 0.0765629736303, 0.996224573858)-72.0007114008, 52.4370521268, -49.3858026235

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Components

#1: Protein PHA synthase


Mass: 66554.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas caviae (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: O32471
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium chloride, glycerol, PEG6000, octyl beta-D-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.999994 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999994 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 59959 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 14.83
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.574 / Num. unique obs: 9640 / CC1/2: 0.816 / Rrim(I) all: 0.677 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
BUCCANEERmodel building
PHENIX1.20.1_4487model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.04 Å / SU ML: 0.4298 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 3808 3.37 %
Rwork0.2101 109092 -
obs0.2115 58604 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12781 0 66 27 12874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004713127
X-RAY DIFFRACTIONf_angle_d0.761217820
X-RAY DIFFRACTIONf_chiral_restr0.05121963
X-RAY DIFFRACTIONf_plane_restr0.00542298
X-RAY DIFFRACTIONf_dihedral_angle_d16.54784791
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.30018052713
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.71729752873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.38661460.36664028X-RAY DIFFRACTION98.17
2.73-2.770.38471330.34424035X-RAY DIFFRACTION98.98
2.77-2.810.39321480.33724102X-RAY DIFFRACTION98.88
2.81-2.850.34161300.30394028X-RAY DIFFRACTION98.72
2.85-2.890.36661550.28384076X-RAY DIFFRACTION98.76
2.89-2.940.31411200.28494100X-RAY DIFFRACTION98.76
2.94-2.980.32231540.28554101X-RAY DIFFRACTION98.98
2.98-3.040.33961300.27734046X-RAY DIFFRACTION98.65
3.04-3.090.32521510.27954034X-RAY DIFFRACTION98.61
3.09-3.150.31911450.28564058X-RAY DIFFRACTION98.48
3.15-3.210.35261320.28974044X-RAY DIFFRACTION98.4
3.21-3.280.38951520.27544075X-RAY DIFFRACTION98.12
3.28-3.360.32911280.24793955X-RAY DIFFRACTION97.63
3.36-3.440.28071620.23133997X-RAY DIFFRACTION97.06
3.44-3.540.26751240.23434050X-RAY DIFFRACTION97.07
3.54-3.640.26371440.22464001X-RAY DIFFRACTION98.11
3.64-3.760.2371340.22124013X-RAY DIFFRACTION97.71
3.76-3.890.27521210.22174014X-RAY DIFFRACTION97.16
3.89-4.050.24041450.20573932X-RAY DIFFRACTION95.97
4.05-4.230.26971610.18684054X-RAY DIFFRACTION98.37
4.23-4.460.22841530.17864044X-RAY DIFFRACTION98.61
4.46-4.740.17471580.16534045X-RAY DIFFRACTION98.82
4.74-5.10.22991360.17214121X-RAY DIFFRACTION98.77
5.1-5.610.21731220.18644035X-RAY DIFFRACTION98.53
5.61-6.420.18731530.20963997X-RAY DIFFRACTION97.49
6.42-8.090.26971440.18884061X-RAY DIFFRACTION98.57

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