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- PDB-7w6c: Crystal structure of a PSH1 in complex with ligand J1K -

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Basic information

Entry
Database: PDB / ID: 7w6c
TitleCrystal structure of a PSH1 in complex with ligand J1K
ComponentsPSH1
KeywordsHYDROLASE / alpha/beta dehydrogenase / plastic degradation / thermo-stable
Function / homology4-(2-hydroxyethylcarbamoyl)benzoic acid
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: PSH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1264
Polymers55,7082
Non-polymers4182
Water2,972165
1
A: PSH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0632
Polymers27,8541
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PSH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0632
Polymers27,8541
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.506, 56.011, 102.321
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PSH1


Mass: 27853.924 Da / Num. of mol.: 2
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-J1K / 4-(2-hydroxyethylcarbamoyl)benzoic acid


Mass: 209.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD, PEG 1500, NaAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 20, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 51681 / % possible obs: 98.3 % / Redundancy: 5.6 % / CC1/2: 0.85 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.46 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 6 / Num. unique obs: 9010 / CC1/2: 0.85 / % possible all: 95.8

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Processing

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

7nei


Resolution: 2.3→29.58 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 2616 5.14 %
Rwork0.236 48273 -
obs0.239 50889 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.78 Å2 / Biso mean: 18.47 Å2 / Biso min: 2.41 Å2
Refinement stepCycle: final / Resolution: 2.3→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 30 165 4107
Biso mean--38.57 17.65 -
Num. residues----514
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 (%)
2.3-2.380.31142360.28434798503496
2.38-2.480.36032580.26574723498197
2.48-2.590.30732560.25294731498797
2.59-2.730.31552680.25864795506399
2.73-2.90.34292760.27194871514799
2.9-3.120.34432660.27274871513799
3.12-3.430.32172740.25614825509999
3.43-3.930.25792520.221748725124100
3.93-4.950.22772570.192749225179100
4.95-29.580.22612730.18554865513899

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