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- PDB-6k3c: Crystal structure of class I PHA synthase (PhaC) mutant from Chro... -

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Basic information

Entry
Database: PDB / ID: 6k3c
TitleCrystal structure of class I PHA synthase (PhaC) mutant from Chromobacterium sp. USM2 bound to Coenzyme A.
ComponentsIntracellular polyhydroxyalkanoate synthase
KeywordsBIOSYNTHETIC PROTEIN / Bioplastic synthase / catalytic domain / CoA binding. / open conformation / open-closed dimer
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acyltransferase activity / cytoplasm
Similarity search - Function
Poly-beta-hydroxybutyrate polymerase, N-terminal domain / Poly(R)-hydroxyalkanoic acid synthase, class I / : / Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
COENZYME A / Intracellular polyhydroxyalkanoate synthase
Similarity search - Component
Biological speciesChromobacterium sp. USM2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.074 Å
AuthorsChek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T.
CitationJournal: Iscience / Year: 2020
Title: Asymmetric Open-Closed Dimer Mechanism of Polyhydroxyalkanoate Synthase PhaC.
Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Tan, H.T. / Sudesh, K. / Hakoshima, T.
History
DepositionMay 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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: Intracellular polyhydroxyalkanoate synthase
B: Intracellular polyhydroxyalkanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4243
Polymers87,6572
Non-polymers7681
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-15 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.802, 61.852, 82.566
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Intracellular polyhydroxyalkanoate synthase


Mass: 43828.410 Da / Num. of mol.: 2 / Mutation: D447N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium sp. USM2 (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: E1APK1
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.074→50 Å / Num. obs: 15234 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.2
Reflection shellResolution: 3.074→3.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.513 / Num. unique obs: 1912 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XAV

5xav


Resolution: 3.074→49.953 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.11
RfactorNum. reflection% reflection
Rfree0.2627 731 4.99 %
Rwork0.2242 --
obs0.2261 14647 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.074→49.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 48 14 5908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046072
X-RAY DIFFRACTIONf_angle_d0.6998287
X-RAY DIFFRACTIONf_dihedral_angle_d15.6162182
X-RAY DIFFRACTIONf_chiral_restr0.046901
X-RAY DIFFRACTIONf_plane_restr0.0041048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0745-3.31180.45021240.35822358X-RAY DIFFRACTION81
3.3118-3.6450.37461470.31412808X-RAY DIFFRACTION96
3.645-4.17220.28771530.24442908X-RAY DIFFRACTION99
4.1722-5.25560.21081510.20322881X-RAY DIFFRACTION98
5.2556-49.95980.21991560.18322961X-RAY DIFFRACTION98

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