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- PDB-7w66: Crystal structure of a PSH1 mutant in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 7w66
TitleCrystal structure of a PSH1 mutant in complex with ligand
ComponentsPSH1
KeywordsHYDROLASE / alpha/beta dehydrogenase / plastic degradation / thermo-stable
Function / homologybis(2-hydroxyethyl) benzene-1,4-dicarboxylate
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsGao, J. / Lara, P. / Li, Z.S. / Han, X. / Wei, R. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2022
Title: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase.
Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / ...Authors: Pfaff, L. / Gao, J. / Li, Z. / Jackering, A. / Weber, G. / Mican, J. / Chen, Y. / Dong, W. / Han, X. / Feiler, C.G. / Ao, Y.F. / Badenhorst, C.P.S. / Bednar, D. / Palm, G.J. / Lammers, M. / Damborsky, J. / Strodel, B. / Liu, W. / Bornscheuer, U.T. / Wei, R.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

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Assembly

Deposited unit
A: PSH1
B: PSH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1123
Polymers55,8582
Non-polymers2541
Water6,539363
1
A: PSH1


Theoretical massNumber of molelcules
Total (without water)27,9291
Polymers27,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PSH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1832
Polymers27,9291
Non-polymers2541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.845, 55.628, 95.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PSH1


Mass: 27928.990 Da / Num. of mol.: 2 / Mutation: L209F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-C8X / bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / bis(2-hydroxyethyl) terephthalate


Mass: 254.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 21% PEG 6000, 0.1M citric acid, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 4, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 74685 / % possible obs: 94.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6004 / CC1/2: 0.797 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NEI

7nei


Resolution: 1.96→30 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 3709 5.02 %
Rwork0.1979 70225 -
obs0.1995 73934 94.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.2 Å2 / Biso mean: 25.6037 Å2 / Biso min: 13.82 Å2
Refinement stepCycle: final / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 18 363 4297
Biso mean--36.5 32.81 -
Num. residues----514
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.96-2.030.3293880.28867431100
2.03-2.110.29033940.25587430100
2.11-2.210.27233930.22787453100
2.21-2.320.27432490.2361470363
2.32-2.470.26863950.21247438100
2.47-2.650.25833700.209713199
2.69-2.930.23453370.20326371100
2.93-3.350.22163860.19237412100
3.35-4.220.19413950.16287465100
4.22-300.19084020.1779739199

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