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- PDB-6ky5: Crystal structure of a hydrolase mutant -

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Basic information

Entry
Database: PDB / ID: 6ky5
TitleCrystal structure of a hydrolase mutant
ComponentsPET hydrolase
KeywordsHYDROLASE / PET hydrolase / mutant
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å
AuthorsCui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Han, J. / Xiang, H. / Chen, Q. / Liu, H.Y. / Han, X. / Liu, W.D. ...Cui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Han, J. / Xiang, H. / Chen, Q. / Liu, H.Y. / Han, X. / Liu, W.D. / Tang, S.Y. / Wu, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31601412 and 31822002 China
CitationJournal: Biorxiv / Year: 2020
Title: Computational redesign of PETase for plasticbiodegradation by GRAPE strategy.
Authors: Cui, Y.L. / Chen, Y.C. / Liu, X.Y. / Dong, S.J. / Tian, Y. / Qiao, Y.X. / Mitra, R. / Han, J. / Li, C.L. / Han, X. / Liu, W.D. / Chen, Q. / Du, W.B. / Tang, S.Y. / Xiang, H. / Liu, H.Y. / Wu, B.
History
DepositionSep 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PET hydrolase
B: PET hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,59919
Polymers62,9662
Non-polymers1,63317
Water9,350519
1
A: PET hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2529
Polymers31,4831
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area9890 Å2
MethodPISA
2
B: PET hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,34810
Polymers31,4831
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.549, 129.789, 51.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-653-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 29 through 292)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 29 - 292 / Label seq-ID: 29 - 292

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 29 through 292)BB

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Components

#1: Protein PET hydrolase


Mass: 31483.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0K8P6T7*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.33 % / Mosaicity: 0.947 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 30, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→25 Å / Num. obs: 71809 / % possible obs: 96.6 % / Redundancy: 9 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Χ2: 0.854 / Net I/σ(I): 14.6 / Num. measured all: 644782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.697.10.52571550.90.2080.5660.77397.6
1.69-1.7680.37871380.9490.140.4040.83397.6
1.76-1.849.30.27571260.9750.0930.2910.94197.1
1.84-1.939.60.19471310.9880.0650.2041.06796.8
1.93-2.059.40.13270950.9940.0440.1390.996.5
2.05-2.219.30.09870670.9960.0330.1040.91795.7
2.21-2.4390.07870700.9970.0270.0820.91595.3
2.43-2.799.10.0670860.9980.0210.0640.81295.2
2.79-3.519.20.04771720.9990.0160.050.64895.2
3.51-259.70.05377690.9960.0180.0560.72299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XH3

5xh3


Resolution: 1.631→24.887 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.51
RfactorNum. reflection% reflection
Rfree0.1823 2000 2.79 %
Rwork0.1688 --
obs0.1692 71722 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.35 Å2 / Biso mean: 25.6233 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: final / Resolution: 1.631→24.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 85 519 4510
Biso mean--49.03 35.83 -
Num. residues----528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1604X-RAY DIFFRACTION7.515TORSIONAL
12B1604X-RAY DIFFRACTION7.515TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.631-1.68910.25521980.218690297
1.6891-1.75670.2131990.1935695698
1.7567-1.83670.2171990.1821692797
1.8367-1.93350.20881990.1767692797
1.9335-2.05450.19471980.174690897
2.0545-2.21310.19541960.1682687396
2.2131-2.43560.19251980.1686686395
2.4356-2.78770.20221980.178688495
2.7877-3.51060.19611990.1676696195
3.5106-24.8870.14462160.1565752199

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