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- PDB-5lul: Structure of a triple variant of cutinase 2 from Thermobifida cel... -

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Basic information

Entry
Database: PDB / ID: 5lul
TitleStructure of a triple 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: 1.9 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Oct 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
B: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6504
Polymers57,5742
Non-polymers762
Water6,828379
1
A: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8272
Polymers28,7871
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8232
Polymers28,7871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.438, 110.438, 75.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

21A-598-

HOH

31B-468-

HOH

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Components

#1: Protein Cutinase 2


Mass: 28787.189 Da / Num. of mol.: 2 / Mutation: R19S, R29N, A30V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida cellulosilytica (bacteria)
Gene: cut2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / Variant (production host): gold / References: UniProt: E9LVH9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L- ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MOPS/HEPES-Na pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.8726 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: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→44.53 Å / Num. obs: 41912 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 14 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 11.1 / CC1/2: 0.978 / % possible all: 99.6

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Processing

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

1jfr


Resolution: 1.9→44.53 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.84
RfactorNum. reflection% reflection
Rfree0.1935 1956 4.67 %
Rwork0.1586 --
obs0.1602 41912 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 2 379 4397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064136
X-RAY DIFFRACTIONf_angle_d0.8145649
X-RAY DIFFRACTIONf_dihedral_angle_d9.6682461
X-RAY DIFFRACTIONf_chiral_restr0.053621
X-RAY DIFFRACTIONf_plane_restr0.006746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.31741370.27292727X-RAY DIFFRACTION96
1.9475-2.00020.19951410.18422833X-RAY DIFFRACTION100
2.0002-2.05910.22991330.16172805X-RAY DIFFRACTION100
2.0591-2.12550.22891440.16742862X-RAY DIFFRACTION100
2.1255-2.20150.21691580.16452801X-RAY DIFFRACTION100
2.2015-2.28960.28151340.18212816X-RAY DIFFRACTION99
2.2896-2.39380.20381420.1592861X-RAY DIFFRACTION100
2.3938-2.520.20921310.16742849X-RAY DIFFRACTION100
2.52-2.67790.21491380.16512861X-RAY DIFFRACTION100
2.6779-2.88460.20511270.16632857X-RAY DIFFRACTION100
2.8846-3.17480.22541480.16632865X-RAY DIFFRACTION100
3.1748-3.63410.16541370.15962881X-RAY DIFFRACTION100
3.6341-4.57780.1521290.12472937X-RAY DIFFRACTION100
4.5778-44.54190.13211570.13513001X-RAY DIFFRACTION100

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