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- PDB-7w69: Crystal structure of a PSH1 mutant in complex with EDO -

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Basic information

Entry
Database: PDB / ID: 7w69
TitleCrystal structure of a PSH1 mutant in complex with EDO
ComponentsPSH1
KeywordsHYDROLASE / alpha/beta dehydrogenase / plastic degradation / thermo-stable
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9912
Polymers27,9291
Non-polymers621
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.526, 55.346, 51.153
Angle α, β, γ (deg.)90.000, 93.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PSH1


Mass: 27928.990 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 24% PEG 4000, 0.1M Nacit, pH5.6, 9% isopropanol

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→25 Å / Num. obs: 42273 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 1.352 / Net I/σ(I): 9.2 / Num. measured all: 397183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.626.40.60841960.8530.2430.6570.64499.1
1.62-1.687.70.53341860.9240.1980.5690.737100
1.68-1.768.90.43742190.9540.1530.4640.87100
1.76-1.859.70.3341860.9750.1110.3481.086100
1.85-1.9710.10.26142260.9840.0870.2761.28100
1.97-2.1210.20.18942070.990.0620.1991.571100
2.12-2.3310.20.15642380.9920.0510.1641.988100
2.33-2.6710.30.11942350.9930.0390.1261.727100
2.67-3.3610.30.09642500.9950.0310.1011.684100
3.36-25100.08143300.9950.0270.0851.37499.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NEI

7nei


Resolution: 1.56→23.52 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 2101 5.01 %
Rwork0.1637 39864 -
obs0.1647 41965 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.63 Å2 / Biso mean: 22.3324 Å2 / Biso min: 10.85 Å2
Refinement stepCycle: final / Resolution: 1.56→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 10 313 2291
Biso mean--47.78 33.86 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.620.22452100.21623946415699
1.62-1.680.22252160.199439604176100
1.68-1.760.23152070.188939754182100
1.76-1.850.22192170.176739514168100
1.85-1.970.22551950.187140194214100
1.97-2.120.19062150.165739624177100
2.12-2.330.19662000.168639674167100
2.33-2.670.20742190.164439824201100
2.67-3.360.16872130.160540104223100
3.36-23.520.14442090.143140924301100

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