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- PDB-5hz2: Crystal structure of PhaC1 from Ralstonia eutropha -

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Basic information

Entry
Database: PDB / ID: 5hz2
TitleCrystal structure of PhaC1 from Ralstonia eutropha
ComponentsPoly-beta-hydroxybutyrate polymerase
KeywordsTRANSFERASE
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(3-hydroxyalkanoate) polymerase subunit PhaC
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / SIR / Resolution: 1.8 Å
AuthorsKim, J. / Kim, K.-J.
CitationJournal: Biotechnol J / Year: 2017
Title: Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms.
Authors: Kim, J. / Kim, Y.J. / Choi, S.Y. / Lee, S.Y. / Kim, K.J.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Poly-beta-hydroxybutyrate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50710
Polymers43,6501
Non-polymers8579
Water5,044280
1
A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,02840
Polymers174,6024
Non-polymers3,42736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area26870 Å2
ΔGint-522 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.246, 87.856, 136.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Poly-beta-hydroxybutyrate polymerase / PHB polymerase / PHB synthase / Poly(3-hydroxyalkanoate) polymerase / PHA polymerase / Poly(3- ...PHB polymerase / PHB synthase / Poly(3-hydroxyalkanoate) polymerase / PHA polymerase / Poly(3-hydroxybutyrate) polymerase / Polyhydroxyalkanoate synthase / PHA synthase


Mass: 43650.387 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP RESIDUES 202-589)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: phbC, H16_A1437 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P23608, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate, HEPES

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.9798
SYNCHROTRONPAL/PLS 7A (6B, 6C1)21.0072
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2701CCDSep 15, 2013Rh coated Torroidal Mirror
ADSC QUANTUM 2702CCDOct 16, 2013Rh coated Torroidal Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
21.00721
ReflectionResolution: 1.8→50 Å / Num. obs: 40301 / % possible obs: 98.1 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 52.17 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.835.10.261193.5
1.83-1.865.60.245194.9
1.86-1.960.217195.2
1.9-1.946.70.194195.6
1.94-1.987.30.171196.8
1.98-2.037.80.158197.6
2.03-2.088.30.135198.3
2.08-2.138.70.122198.4
2.13-2.29.30.109198.5
2.2-2.279.80.099198.7
2.27-2.3510.10.087198.7
2.35-2.4410.60.081199
2.44-2.5511.10.071199.5
2.55-2.6911.60.068199.5
2.69-2.8611.80.061199.7
2.86-3.0812.50.057199.4
3.08-3.3912.90.051199.6
3.39-3.8813.30.046199.8
3.88-4.8813.40.043199.7
4.88-5012.40.045199.1

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Phasing

PhasingMethod: SIR
Phasing dmFOM : 0.68 / FOM acentric: 0.69 / FOM centric: 0.57 / Reflection: 29169 / Reflection acentric: 26571 / Reflection centric: 2598

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVE2.15model building
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.477 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 2001 5 %RANDOM
Rwork0.1515 ---
obs0.1534 38300 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 30.381 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0 Å2
2---0.83 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 47 280 3340
Biso mean--56.38 37.88 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193142
X-RAY DIFFRACTIONr_bond_other_d0.0020.022919
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.954306
X-RAY DIFFRACTIONr_angle_other_deg1.19636686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99423.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6521518
X-RAY DIFFRACTIONr_chiral_restr0.1920.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02742
X-RAY DIFFRACTIONr_mcbond_it2.6112.7661551
X-RAY DIFFRACTIONr_mcbond_other2.62.7651550
X-RAY DIFFRACTIONr_mcangle_it3.5594.1351937
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 130 -
Rwork0.248 2688 -
all-2818 -
obs--93.34 %

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