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- PDB-6sbn: Polyester hydrolase PE-H of Pseudomonas aestusnigri -

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Basic information

Entry
Database: PDB / ID: 6sbn
TitlePolyester hydrolase PE-H of Pseudomonas aestusnigri
Componentspolyester hydrolase
KeywordsHYDROLASE / polyester degradation / PET hydrolase / marine bacteria / Pseudomonas aestusnigri
Function / homology
Function and homology information


Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DLH domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aestusnigri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsBollinger, A. / Thies, S. / Kobus, S. / Hoeppner, A. / Smits, S.H.J. / Jaeger, K.-E.
CitationJournal: Front Microbiol / Year: 2020
Title: A Novel Polyester Hydrolase From the Marine BacteriumPseudomonas aestusnigri -Structural and Functional Insights.
Authors: Bollinger, A. / Thies, S. / Knieps-Grunhagen, E. / Gertzen, C. / Kobus, S. / Hoppner, A. / Ferrer, M. / Gohlke, H. / Smits, S.H.J. / Jaeger, K.E.
History
DepositionJul 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polyester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4873
Polymers33,4051
Non-polymers822
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-6 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.814, 80.014, 88.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein polyester hydrolase


Mass: 33405.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aestusnigri (bacteria) / Gene: B7O88_11480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H6AD45
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 4.5, 16 % (w/v) PEG 3000, 0.036 mM lyso-Foscholine14

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 1.09→50 Å / Num. obs: 101774 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rsym value: 0.076 / Net I/σ(I): 16.2
Reflection shellResolution: 1.09→1.16 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 16134 / Rsym value: 0.43 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→45 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.628 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.023
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.137 2100 2.1 %RANDOM
Rwork0.1069 ---
obs0.1075 99673 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 179.47 Å2 / Biso mean: 13.219 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.09→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 5 368 2356
Biso mean--16.42 26.26 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192104
X-RAY DIFFRACTIONr_bond_other_d0.0050.021894
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.9452877
X-RAY DIFFRACTIONr_angle_other_deg1.54534376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96322.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20415317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5221516
X-RAY DIFFRACTIONr_chiral_restr0.1930.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212464
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02510
X-RAY DIFFRACTIONr_rigid_bond_restr6.27233997
X-RAY DIFFRACTIONr_sphericity_free27.42585
X-RAY DIFFRACTIONr_sphericity_bonded12.67554218
LS refinement shellResolution: 1.09→1.118 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.185 151 -
Rwork0.154 7185 -
obs--97.62 %

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