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- PDB-5t6o: Structure of the catalytic domain of the class I polyhydroxybutyr... -

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Basic information

Entry
Database: PDB / ID: 5t6o
TitleStructure of the catalytic domain of the class I polyhydroxybutyrate synthase from Cupriavidus necator
ComponentsPoly-beta-hydroxybuterate polymerase
KeywordsBIOSYNTHETIC PROTEIN / polyhydroxybutyrate synthase / PhaC / alpha/beta hydrolase fold / nontemplate-dependent polymerization / TRANSFERASE
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly-beta-hydroxybuterate polymerase / Poly(3-hydroxyalkanoate) polymerase subunit PhaC
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWittenborn, E.C. / Jost, M. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of the Catalytic Domain of the Class I Polyhydroxybutyrate Synthase from Cupriavidus necator.
Authors: Wittenborn, E.C. / Jost, M. / Wei, Y. / Stubbe, J. / Drennan, C.L.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly-beta-hydroxybuterate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0195
Polymers42,6351
Non-polymers3844
Water5,098283
1
A: Poly-beta-hydroxybuterate polymerase
hetero molecules

A: Poly-beta-hydroxybuterate polymerase
hetero molecules

A: Poly-beta-hydroxybuterate polymerase
hetero molecules

A: Poly-beta-hydroxybuterate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,07820
Polymers170,5414
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area15850 Å2
ΔGint-83 kcal/mol
Surface area48360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.080, 87.820, 137.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-884-

HOH

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Components

#1: Protein Poly-beta-hydroxybuterate polymerase


Mass: 42635.242 Da / Num. of mol.: 1 / Fragment: UNP residues 201-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: D3UAK8, UniProt: P23608*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.9 M ammonium sulfate, 0.1 M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 40649 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rsym value: 0.046 / Net I/σ(I): 25.76
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.24 / CC1/2: 0.762 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4-1496refinement
XDS20141103data reduction
XSCALE20141103data scaling
SHELXDE97-2.20090721phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→73.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.1997 2032 5 %
Rwork0.1715 --
obs0.1729 40645 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→73.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 20 283 3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063051
X-RAY DIFFRACTIONf_angle_d0.8214197
X-RAY DIFFRACTIONf_dihedral_angle_d13.1841748
X-RAY DIFFRACTIONf_chiral_restr0.054465
X-RAY DIFFRACTIONf_plane_restr0.006538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.28721330.25112539X-RAY DIFFRACTION100
1.8419-1.88790.28251340.24092535X-RAY DIFFRACTION100
1.8879-1.9390.31221350.25022568X-RAY DIFFRACTION100
1.939-1.99610.22311330.19182527X-RAY DIFFRACTION100
1.9961-2.06050.25171340.19182538X-RAY DIFFRACTION100
2.0605-2.13410.21841340.17472553X-RAY DIFFRACTION100
2.1341-2.21960.22991350.1792559X-RAY DIFFRACTION100
2.2196-2.32060.26451340.18642552X-RAY DIFFRACTION100
2.3206-2.4430.19851340.17342546X-RAY DIFFRACTION100
2.443-2.5960.2311360.17332583X-RAY DIFFRACTION100
2.596-2.79650.20921350.18592562X-RAY DIFFRACTION100
2.7965-3.07790.21261370.18642595X-RAY DIFFRACTION100
3.0779-3.52330.20951370.17412601X-RAY DIFFRACTION100
3.5233-4.43890.14291380.14012623X-RAY DIFFRACTION100
4.4389-74.01210.16761430.1532732X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 86.6891 Å / Origin y: 28.4958 Å / Origin z: 18.1841 Å
111213212223313233
T0.1813 Å2-0.0151 Å20.001 Å2-0.1893 Å2-0.0036 Å2--0.1864 Å2
L0.6131 °2-0.1179 °20.1081 °2-1.0266 °20.1514 °2--1.0579 °2
S0.0024 Å °0.0106 Å °-0.0203 Å °0.0038 Å °0.07 Å °-0.1317 Å °-0.0236 Å °0.0942 Å °-0.0698 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 201 through 589)

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