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

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Basic information

Entry
Database: PDB / ID: 9kqz
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
Function / homologyACETATE ION
Function and homology information
Biological speciesComamonas sp. NyZ500 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,8808
Polymers42,5161
Non-polymers3647
Water10,917606
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)164.686, 164.686, 164.686
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-829-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SGNH/GDSL hydrolase family protein


Mass: 42515.523 Da / Num. of mol.: 1 / Mutation: S227A
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)

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Non-polymers , 6 types, 613 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate

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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: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→19.76 Å / Num. obs: 56919 / % possible obs: 99.75 % / Redundancy: 38.1 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.027 / Net I/σ(I): 19
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.77 / Num. unique obs: 5540 / Rpim(I) all: 0.165 / % possible all: 97.28

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→19.68 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 15.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1627 2773 5.06 %
Rwork0.1425 --
obs0.1436 54811 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 19 606 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073069
X-RAY DIFFRACTIONf_angle_d0.7914203
X-RAY DIFFRACTIONf_dihedral_angle_d20.1461084
X-RAY DIFFRACTIONf_chiral_restr0.055500
X-RAY DIFFRACTIONf_plane_restr0.004552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.60961360.57992562X-RAY DIFFRACTION94
1.95-1.980.28641110.22992702X-RAY DIFFRACTION99
1.98-2.020.17731160.15952642X-RAY DIFFRACTION98
2.02-2.060.17721440.14082665X-RAY DIFFRACTION99
2.06-2.110.15361250.13932624X-RAY DIFFRACTION98
2.11-2.150.16851530.14252620X-RAY DIFFRACTION98
2.16-2.210.16131540.14252587X-RAY DIFFRACTION97
2.21-2.270.19041130.13732662X-RAY DIFFRACTION97
2.27-2.330.1671260.13322641X-RAY DIFFRACTION97
2.34-2.410.17371530.13352621X-RAY DIFFRACTION97
2.41-2.50.15851480.14452609X-RAY DIFFRACTION97
2.5-2.60.16371420.13772605X-RAY DIFFRACTION97
2.6-2.710.1761240.13782613X-RAY DIFFRACTION96
2.71-2.860.18141640.14622599X-RAY DIFFRACTION97
2.86-3.030.17221470.14292599X-RAY DIFFRACTION96
3.04-3.270.14741310.13832569X-RAY DIFFRACTION95
3.27-3.590.14591660.13472559X-RAY DIFFRACTION95
3.6-4.110.13311650.11432532X-RAY DIFFRACTION94
4.11-5.160.12021240.11212556X-RAY DIFFRACTION92
5.17-19.680.1411310.13912471X-RAY DIFFRACTION87

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