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- PDB-4cg3: Structural and functional studies on a thermostable polyethylene ... -

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Basic information

Entry
Database: PDB / ID: 4cg3
TitleStructural and functional studies on a thermostable polyethylene therephtalate degrading hydrolase from Thermobifida fusca
ComponentsCUTINASE
KeywordsHYDROLASE / PET DEGRADATION / ALPHA-BETA- FOLD
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / periplasmic space / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRoth, C. / Wei, R. / Oeser, T. / Then, J. / Foellner, C. / Zimmermann, W. / Straeter, N.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2014
Title: Structural and Functional Studies on a Thermostable Polyethylene Terephthalate Degrading Hydrolase from Thermobifida Fusca.
Authors: Roth, C. / Wei, R. / Oeser, T. / Then, J. / Follner, C. / Zimmermann, W. / Strater, N.
History
DepositionNov 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8862
Polymers33,7901
Non-polymers961
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.900, 117.900, 36.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Number of models77

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Components

#1: Protein CUTINASE


Mass: 33789.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Strain: KW3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E5BBQ3, cutinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.55→23 Å / Num. obs: 36710 / % possible obs: 100 % / Observed criterion σ(I): 2.55 / Redundancy: 3.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JFR

1jfr


Resolution: 1.55→23.122 Å / SU ML: 0.11 / σ(F): 1.24 / Phase error: 13.59 / Stereochemistry target values: ML / Details: REFINED USING PHENIX.ENSEMBLE REFINEMENT
RfactorNum. reflection% reflection
Rfree0.1492 3279 8.9 %
Rwork0.1173 --
obs0.1202 36710 99.93 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.55→23.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 5 99 2115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57320.25831440.19351451X-RAY DIFFRACTION100
1.5732-1.59780.21741330.18051421X-RAY DIFFRACTION100
1.5978-1.62390.20781310.15651466X-RAY DIFFRACTION100
1.6239-1.65190.20321450.15751423X-RAY DIFFRACTION100
1.6519-1.6820.20911420.15031439X-RAY DIFFRACTION100
1.682-1.71430.19271540.15041450X-RAY DIFFRACTION100
1.7143-1.74930.20021340.14461461X-RAY DIFFRACTION100
1.7493-1.78730.17231380.14191429X-RAY DIFFRACTION100
1.7873-1.82890.1671270.13141439X-RAY DIFFRACTION100
1.8289-1.87460.16381460.11931460X-RAY DIFFRACTION100
1.8746-1.92520.13841260.11131464X-RAY DIFFRACTION100
1.9252-1.98190.15741630.10141425X-RAY DIFFRACTION100
1.9819-2.04580.1461440.11429X-RAY DIFFRACTION100
2.0458-2.11890.13841440.10091449X-RAY DIFFRACTION100
2.1189-2.20360.14221470.09761455X-RAY DIFFRACTION100
2.2036-2.30380.13641610.09951442X-RAY DIFFRACTION100
2.3038-2.42520.13881290.10211482X-RAY DIFFRACTION100
2.4252-2.57690.11741400.10291441X-RAY DIFFRACTION100
2.5769-2.77560.14341510.11371453X-RAY DIFFRACTION100
2.7756-3.05440.151370.12411478X-RAY DIFFRACTION100
3.0544-3.4950.15271660.12021431X-RAY DIFFRACTION100
3.495-4.39840.1351270.10691519X-RAY DIFFRACTION100
4.3984-23.12470.12711500.12231524X-RAY DIFFRACTION99

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