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- PDB-8qrj: LCC-ICCG PETase mutant H218Y -

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Basic information

Entry
Database: PDB / ID: 8qrj
TitleLCC-ICCG PETase mutant H218Y
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / LCC / PETase / direct enzyme evolution
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Alpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Leaf-branch compost cutinase
Similarity search - Component
Biological speciesunidentified prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsOrr, G. / Niv, Y. / Barakat, M. / Boginya, A. / Dessau, M. / Afriat-Jurnou, L.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation401/18 Israel
CitationJournal: Biotechnol J / Year: 2024
Title: Streamlined screening of extracellularly expressed PETase libraries for improved polyethylene terephthalate degradation.
Authors: Orr, G. / Niv, Y. / Barakat, M. / Boginya, A. / Dessau, M. / Afriat-Jurnou, L.
History
DepositionOct 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8414
Polymers31,4121
Non-polymers4293
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area10000 Å2
Unit cell
Length a, b, c (Å)81.900, 94.510, 80.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Leaf-branch compost cutinase


Mass: 31412.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified prokaryotic organism (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: G9BY57
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.3 / Details: 20% PEG 3350, 0.2 M Na-formate pH=7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 93953 / % possible obs: 82 % / Redundancy: 1.77 % / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.13 / Net I/σ(I): 4.65
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.42-1.460.89468630.3141.1751
1.46-1.50.76665260.4091.0091
1.5-1.540.58762210.5630.7721
1.54-1.590.51664050.6150.6761
1.59-1.640.46462130.6740.6121
1.64-1.70.36359730.7440.481
1.7-1.760.31359370.8020.411
1.76-1.830.25757530.8630.3361
1.83-1.910.20254060.9050.2641
1.91-2.010.16852620.9310.221
2.01-2.120.1349690.9580.1711
2.12-2.250.11147500.9710.1461
2.25-2.40.143320.9750.1321
2.4-2.590.08439110.980.1121
2.59-2.840.07736500.9840.1011
2.84-3.180.06232830.9890.0811
3.18-3.670.04529070.9930.0591
3.67-4.490.03825500.9960.0491
4.49-6.350.03920010.9960.0511

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→49.17 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 2868 5.07 %
Rwork0.1669 --
obs0.1676 56565 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 27 442 2410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062046
X-RAY DIFFRACTIONf_angle_d0.8262799
X-RAY DIFFRACTIONf_dihedral_angle_d11.49738
X-RAY DIFFRACTIONf_chiral_restr0.078315
X-RAY DIFFRACTIONf_plane_restr0.01365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.35591340.30762631X-RAY DIFFRACTION95
1.47-1.50.31251530.26962599X-RAY DIFFRACTION93
1.5-1.530.26311370.25882601X-RAY DIFFRACTION93
1.53-1.560.25921440.2482628X-RAY DIFFRACTION94
1.56-1.60.26691430.24472693X-RAY DIFFRACTION96
1.6-1.640.26931400.23522653X-RAY DIFFRACTION95
1.64-1.680.25671500.21742625X-RAY DIFFRACTION94
1.68-1.730.20561490.19772704X-RAY DIFFRACTION97
1.73-1.790.22171420.18142729X-RAY DIFFRACTION97
1.79-1.850.17971320.17182698X-RAY DIFFRACTION96
1.85-1.930.20181440.17132724X-RAY DIFFRACTION97
1.93-2.010.1851480.16152701X-RAY DIFFRACTION96
2.02-2.120.17441460.14592714X-RAY DIFFRACTION96
2.12-2.250.15641360.13732724X-RAY DIFFRACTION96
2.25-2.430.14561530.14422710X-RAY DIFFRACTION96
2.43-2.670.17321620.14982658X-RAY DIFFRACTION94
2.67-3.060.17931540.15062701X-RAY DIFFRACTION95
3.06-3.850.14261250.13982716X-RAY DIFFRACTION93
3.85-49.170.12731460.13772851X-RAY DIFFRACTION95
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)
11.1431-0.1389-0.00131.79110.38591.44970.00790.01690.095-0.0649-0.00280.0721-0.0448-0.0395-0.0060.09160.00990.00050.10260.01710.092225.430525.647523.3517
20.7378-0.30490.28252.7892-0.96220.80280.0170.0114-0.00370.03190.06090.1670.0269-0.1076-0.07970.1120.0020.00060.12140.00270.105921.836516.455129.2542
30.2354-0.1130.28027.8782-2.0081.30970.0377-0.0196-0.0468-0.10290.03080.23830.1546-0.0633-0.07940.11430.00020.00130.110.00520.112926.384410.007826.5078
40.27090.3191-0.3831.2247-0.35550.55140.02810.0165-0.015-0.0723-0.0359-0.02510.02080.01860.02570.10660.006-0.00380.12920.00420.113734.408116.696721.7311
50.96190.0529-0.59550.8518-0.06371.5944-0.0034-0.0673-0.01890.0612-0.0036-0.03320.06850.09550.01390.09580.0044-0.00460.09930.00280.107732.236714.427542.021
60.74080.31950.35451.8108-0.00772.67090.05-0.05750.1307-0.0309-0.02170.11160.0836-0.221-0.00540.0732-0.01130.01070.1128-0.00720.13216.005915.989340.8143
70.60510.2911-0.71320.8719-0.64652.25650.0861-0.09620.10670.092-0.0367-0.019-0.22230.1221-0.05780.1162-0.00620.0120.1074-0.0190.116928.514829.206541.9501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 158 )
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 249 )
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 292 )

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