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- PDB-5luk: Structure of a double variant of cutinase 2 from Thermobifida cel... -

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Basic information

Entry
Database: PDB / ID: 5luk
TitleStructure of a double variant of cutinase 2 from Thermobifida cellulosilytica
ComponentsCutinase 2
KeywordsHYDROLASE / cutinase / alpha/beta hydrolase / poly(ethyleneterephthlate) (PET)
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 cellulosilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHromic, A. / Lyskowski, A. / Gruber, K.
Funding support Austria, 6items
OrganizationGrant numberCountry
Federal Ministry of Science, Research and Economy (BMWFW) Austria
Federal Ministry of Traffic, Innovation and Technology (bmvit) Austria
Styrian Business Promotion Agency SFG Austria
Standortagentur Tirol Austria
Government of Lower Austria and Business Agency Vienna Austria
Austrian Research Promotion Agency FFG Austria
CitationJournal: Biotechnol. Bioeng. / Year: 2017
Title: Small cause, large effect: Structural characterization of cutinases from Thermobifida cellulosilytica.
Authors: Ribitsch, D. / Hromic, A. / Zitzenbacher, S. / Zartl, B. / Gamerith, C. / Pellis, A. / Jungbauer, A. / yskowski, A. / Steinkellner, G. / Gruber, K. / Tscheliessnig, R. / Herrero Acero, E. / Guebitz, G.M.
History
DepositionSep 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 23, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0126
Polymers28,8571
Non-polymers1555
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-41 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.595, 50.512, 105.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cutinase 2 / Cutinase


Mass: 28857.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida cellulosilytica (bacteria)
Gene: cut2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: E9LVH9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.87 Å3/Da / Density % sol: 34.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 1.1 M Sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, and 0.5% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.45→37.9 Å / Num. obs: 38429 / % possible obs: 98 % / Redundancy: 8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5 / CC1/2: 0.948 / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX1.8.4-1496refinement
XDSdata reduction
XDSdata scaling
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFR

1jfr


Resolution: 1.45→37.886 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.74
RfactorNum. reflection% reflection
Rfree0.1638 1888 4.91 %
Rwork0.1442 --
obs0.1452 38429 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 5 198 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062118
X-RAY DIFFRACTIONf_angle_d0.9432897
X-RAY DIFFRACTIONf_dihedral_angle_d14.171787
X-RAY DIFFRACTIONf_chiral_restr0.084316
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4484-1.48750.17371250.15452297X-RAY DIFFRACTION82
1.4875-1.53130.16331430.1462542X-RAY DIFFRACTION90
1.5313-1.58070.17281250.14342788X-RAY DIFFRACTION97
1.5807-1.63720.17061520.14042821X-RAY DIFFRACTION100
1.6372-1.70280.16351520.13982857X-RAY DIFFRACTION100
1.7028-1.78030.17951380.14212839X-RAY DIFFRACTION100
1.7803-1.87410.17481510.13792870X-RAY DIFFRACTION100
1.8741-1.99160.18091580.14152837X-RAY DIFFRACTION100
1.9916-2.14530.15681610.13732875X-RAY DIFFRACTION100
2.1453-2.36120.16981400.14082880X-RAY DIFFRACTION100
2.3612-2.70280.17941450.1492927X-RAY DIFFRACTION100
2.7028-3.40490.13111460.14882955X-RAY DIFFRACTION100
3.4049-37.89890.16251520.14673053X-RAY DIFFRACTION99

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