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- PDB-4cg1: Structural and functional studies on a thermostable polyethylene ... -

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Basic information

Entry
Database: PDB / ID: 4cg1
TitleStructural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca
ComponentsCUTINASE
KeywordsHYDROLASE / PET DEGRADATION / ALPHA BETA FOLD
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region
Similarity search - Function
Chlorophyllase / Chlorophyllase / Cutinase / : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8273
Polymers30,6351
Non-polymers1922
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.675, 116.675, 35.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

21A-2209-

HOH

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Components

#1: Protein CUTINASE


Mass: 30635.193 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.15 Å3/Da / Density % sol: 49.92 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→41 Å / Num. obs: 118918 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 4.8 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.5 / % possible all: 87

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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: 1.4→41.251 Å / SU ML: 0.14 / σ(F): 0.83 / Phase error: 14.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 1907 2.1 %
Rwork0.1356 --
obs0.136 91150 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 10 340 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072114
X-RAY DIFFRACTIONf_angle_d1.2092902
X-RAY DIFFRACTIONf_dihedral_angle_d11.292774
X-RAY DIFFRACTIONf_chiral_restr0.074325
X-RAY DIFFRACTIONf_plane_restr0.008378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.26521310.2296331X-RAY DIFFRACTION97
1.435-1.47390.22551130.20666344X-RAY DIFFRACTION98
1.4739-1.51720.23091490.18596357X-RAY DIFFRACTION98
1.5172-1.56620.22611600.17326337X-RAY DIFFRACTION98
1.5662-1.62220.19621250.16116370X-RAY DIFFRACTION98
1.6222-1.68710.17491190.15216404X-RAY DIFFRACTION98
1.6871-1.76390.15111420.13326382X-RAY DIFFRACTION98
1.7639-1.85690.14921560.12596324X-RAY DIFFRACTION99
1.8569-1.97320.15181460.11376421X-RAY DIFFRACTION98
1.9732-2.12560.12581540.11066363X-RAY DIFFRACTION99
2.1256-2.33950.12311370.10736457X-RAY DIFFRACTION99
2.3395-2.6780.15151050.11556383X-RAY DIFFRACTION99
2.678-3.37370.16561310.12816441X-RAY DIFFRACTION99
3.3737-41.26870.12161390.13166329X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.078-0.0696-0.07950.12330.00470.19990.07130.07830.0722-0.0398-0.02560.0977-0.0783-0.07940.0220.04820.00140.00190.0658-0.00020.096150.351544.42835.8105
20.05760.08230.02160.17940.07990.06070.0210.0590.0984-0.0515-0.00970.0216-0.0559-0.0204-0.00010.04950.00690.00940.04660.01310.05158.241943.98283.573
30.02060.0187-0.00840.02170.00720.01970.0487-0.03160.05270.053-0.027-0.0427-0.05060.033700.0596-0.00240.00870.0499-0.00460.059166.48243.522211.8446
40.0850.08010.04330.0890.0280.02070.00040.00050.04510.0073-0.02020.06660.00520.021-0.00110.0613-0.00140.00780.0402-0.00140.045956.302346.076912.8536
50.2163-0.0216-0.02540.10450.00880.05140.0222-0.0014-0.05880.0061-0.0216-0.01630.03010.02510.00120.05420.0023-0.00220.03840.0050.024363.874726.55267.6868
60.0267-0.0408-0.05660.42270.12050.17180.04690.1071-0.0634-0.0746-0.05980.16490.0768-0.0789-0.05450.07290.0219-0.02620.0719-0.01340.03253.594131.44220.4025
70.1116-0.1021-0.03240.20040.03470.01110.00670.0689-0.1259-0.0433-0.01670.20680.0583-0.06340.00780.0764-0.0133-0.01570.0614-0.01290.126247.674323.42236.765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 40 THROUGH 92 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 93 THROUGH 109 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 110 THROUGH 130 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 131 THROUGH 203 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 204 THROUGH 230 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 231 THROUGH 263 )

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