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- PDB-9knk: Crystal structure of full-length PHA synthase (PhaC) from Aeromon... -

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Basic information

Entry
Database: PDB / ID: 9knk
TitleCrystal structure of full-length PHA synthase (PhaC) from Aeromonas caviae
ComponentsPHA synthase
KeywordsBIOSYNTHETIC PROTEIN / PHA synthase / full-length PhaC / dimer / tunnel / catalytic triad / polyhydroxyalkanoates
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: 3.29 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)21K15028 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


Theoretical massNumber of molelcules
Total (without water)199,6633
Polymers199,6633
Non-polymers00
Water1267
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)156.632, 96.300, 142.999
Angle α, β, γ (deg.)90.000, 90.460, 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 6 through 18 or (resid 19...
d_2ens_1(chain "B" and (resid 6 through 69 or (resid 70...
d_3ens_1(chain "C" and (resid 6 through 22 or (resid 23...

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_11TYRTYRASPASPAA6 - 418 - 43
d_12PROPROLYSLYSAA54 - 7856 - 80
d_13GLNGLNTHRTHRAA105 - 167107 - 169
d_14GLYGLYASNASNAA172 - 194174 - 196
d_15ALAALAGLUGLUAA202 - 358204 - 360
d_16ILEILEGLUGLUAA361 - 395363 - 397
d_17SERSERTHRTHRAA397 - 456399 - 458
d_18ILEILEASNASNAA458 - 521460 - 523
d_19ALAALAARGARGAA525 - 553527 - 555
d_110GLUGLUPROPROAA558 - 583560 - 585
d_21TYRTYRTHRTHRBB6 - 1678 - 169
d_22GLYGLYASNASNBB172 - 194174 - 196
d_23ALAALAGLUGLUBB202 - 358204 - 360
d_24ILEILEGLUGLUBB361 - 395363 - 397
d_25SERSERTHRTHRBB397 - 456399 - 458
d_26ILEILEASNASNBB458 - 521460 - 523
d_27ALAALAARGARGBB525 - 553527 - 555
d_28GLUGLUPROPROBB558 - 583560 - 585
d_31TYRTYRASPASPCC6 - 418 - 43
d_32PROPROLYSLYSCC54 - 7856 - 80
d_33GLNGLNASNASNCC105 - 194107 - 196
d_34ALAALAARGARGCC202 - 553204 - 555
d_35GLUGLUPROPROCC558 - 583560 - 585

NCS oper:
IDCodeMatrixVector
1given(0.455321751214, -0.890060249875, -0.0217911556209), (-0.888200592652, -0.452407668221, -0.0801686281998), (0.0614964233454, 0.0558574375214, -0.996543093192)91.1683518344, 63.2786990192, 93.2558648564
2given(-0.445572700516, -0.893455159888, 0.056593690672), (0.894495176842, -0.44172059737, 0.069002119284), (-0.0366517006665, 0.0813682439765, 0.996009970688)84.1856995997, 52.9285098984, -49.9677743138

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 3.29→50 Å / Num. obs: 31906 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 111.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.083 / Net I/σ(I): 11.14
Reflection shellResolution: 3.29→3.42 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.508 / Num. unique obs: 5017 / CC1/2: 0.814 / Rrim(I) all: 0.604 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUCCANEERmodel building
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→47.66 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1592 4.99 %
Rwork0.1927 30285 -
obs0.1948 31877 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.02 Å2
Refinement stepCycle: LAST / Resolution: 3.29→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12289 0 0 7 12296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002612574
X-RAY DIFFRACTIONf_angle_d0.584917165
X-RAY DIFFRACTIONf_chiral_restr0.04031948
X-RAY DIFFRACTIONf_plane_restr0.00422218
X-RAY DIFFRACTIONf_dihedral_angle_d4.01341700
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.31466533042
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.956318914861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.40.31431390.27392635X-RAY DIFFRACTION94.19
3.4-3.520.29821440.24292761X-RAY DIFFRACTION99.69
3.52-3.660.31651460.24582763X-RAY DIFFRACTION99.08
3.66-3.830.26151440.22432758X-RAY DIFFRACTION98.71
3.83-4.030.26971460.2082767X-RAY DIFFRACTION99.25
4.03-4.280.27581420.19452734X-RAY DIFFRACTION98.93
4.28-4.610.22381470.17612792X-RAY DIFFRACTION98.76
4.61-5.080.21341440.17272736X-RAY DIFFRACTION98.19
5.08-5.810.2781460.19522760X-RAY DIFFRACTION98.71
5.81-7.310.22041450.21692765X-RAY DIFFRACTION97.59
7.32-47.660.18281490.16212814X-RAY DIFFRACTION97.5

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