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- PDB-9kr0: Structural Basis for the Polymer-Protein Binding Mechanism of Pol... -

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Basic information

Entry
Database: PDB / ID: 9kr0
TitleStructural Basis for the Polymer-Protein Binding Mechanism of Polyvinyl Alcohol Esterase
ComponentsSGNH/GDSL hydrolase family protein
KeywordsHYDROLASE / Polyvinyl alcohol / degradation / complex structure / molecular mechanism
Biological speciesComamonas sp. NyZ500 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWu, Y.F. / Xu, X.X. / Yin, C.F. / Wang, L.T. / Zhou, N.Y. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Key R&D Program of China2021YFA0909500 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural Basis for the Enzyme-Polymer Binding Mechanism of Poly(vinyl alcohol) Esterase
Authors: Wu, Y. / Xu, X. / Yin, C.F. / Shen, Z. / Wang, L. / Zhou, N.Y. / Zhou, J.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7163
Polymers42,5321
Non-polymers1842
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.000, 164.000, 164.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-757-

HOH

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Components

#1: Protein SGNH/GDSL hydrolase family protein


Mass: 42531.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Comamonas sp. NyZ500' is not available in UniProt at the time of biocuration. The reference sequence from NCBI (id: WP_202789293.1).
Source: (gene. exp.) Comamonas sp. NyZ500 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 4.32 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M Sodium formate, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→38.66 Å / Num. obs: 67659 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Net I/σ(I): 28.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.38 / Num. unique obs: 4022 / CC1/2: 0.954 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.66 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1597 3333 4.93 %
Rwork0.1533 --
obs0.1536 67606 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 12 406 3315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.93
X-RAY DIFFRACTIONf_dihedral_angle_d11.9881101
X-RAY DIFFRACTIONf_chiral_restr0.063504
X-RAY DIFFRACTIONf_plane_restr0.007559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.23911190.20182726X-RAY DIFFRACTION100
1.83-1.850.17391200.18462648X-RAY DIFFRACTION100
1.85-1.880.19071210.16632673X-RAY DIFFRACTION100
1.88-1.910.16221500.16452625X-RAY DIFFRACTION100
1.91-1.950.16841420.15492688X-RAY DIFFRACTION100
1.95-1.980.16611570.14872648X-RAY DIFFRACTION100
1.98-2.020.16351580.14662638X-RAY DIFFRACTION100
2.02-2.060.14491200.13782669X-RAY DIFFRACTION100
2.06-2.110.17341440.14742664X-RAY DIFFRACTION100
2.11-2.150.15521460.15082653X-RAY DIFFRACTION100
2.15-2.210.16741450.15032659X-RAY DIFFRACTION100
2.21-2.270.16661370.14942667X-RAY DIFFRACTION100
2.27-2.330.15131270.15012656X-RAY DIFFRACTION100
2.33-2.410.17491380.15742691X-RAY DIFFRACTION100
2.41-2.50.14931360.16252693X-RAY DIFFRACTION100
2.5-2.60.17911260.16042649X-RAY DIFFRACTION100
2.6-2.710.1761550.16982676X-RAY DIFFRACTION100
2.71-2.860.1651360.17192673X-RAY DIFFRACTION100
2.86-3.040.16751460.16292689X-RAY DIFFRACTION100
3.04-3.270.15771580.16392661X-RAY DIFFRACTION100
3.27-3.60.17011330.14762692X-RAY DIFFRACTION100
3.6-4.120.13161330.12852725X-RAY DIFFRACTION100
4.12-5.190.13471520.12852698X-RAY DIFFRACTION100
5.19-38.660.14751340.16282812X-RAY DIFFRACTION100

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