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- PDB-9kr3: Structural Basis for the Polymer-Protein Binding Mechanism of Pol... -

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Basic information

Entry
Database: PDB / ID: 9kr3
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 / homology:
Function and homology information
Biological speciesComamonas sp. NyZ500 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)43,1574
Polymers42,5161
Non-polymers6423
Water11,043613
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)164.790, 164.790, 164.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

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Components

#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)
#2: Chemical ChemComp-A1EGL / [(2S,4S,6S,8S,10R,12R,14R,16R,18R,20R)-12-acetyloxy-2,4,6,10,14,16,18,20,22-nonakis(oxidanyl)docosan-8-yl] ethanoate


Mass: 570.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
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: 4.39 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride

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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: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→47.57 Å / Num. obs: 70980 / % possible obs: 100 % / Redundancy: 16.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 1.458 / Mean I/σ(I) obs: 2 / Num. unique obs: 4055 / CC1/2: 0.734 / Rpim(I) all: 0.531

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→47.57 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 3430 4.83 %
Rwork0.1571 67542 -
obs0.1581 70972 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.25 Å2 / Biso mean: 24.8566 Å2 / Biso min: 13.62 Å2
Refinement stepCycle: final / Resolution: 1.78→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 41 613 3550
Biso mean--47.95 36.3 -
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.78-1.810.22911680.230427932961
1.81-1.830.22481580.200328012959
1.83-1.860.2431550.196327682923
1.86-1.890.24331410.200427772918
1.89-1.920.26811520.209927742926
1.92-1.960.2491400.18928192959
1.96-20.18081460.180427802926
2-2.040.19281160.165128342950
2.04-2.080.17841460.152227942940
2.08-2.130.17731460.152127992945
2.13-2.180.17581370.154827712908
2.18-2.240.18271520.152828152967
2.24-2.310.17071420.154327932935
2.31-2.380.17921200.157128312951
2.38-2.470.19211190.169128202939
2.47-2.570.20341430.174828152958
2.57-2.680.19771360.168528362972
2.68-2.830.1981360.17828042940
2.83-30.16191080.172528652973
3-3.230.18931540.160428262980
3.24-3.560.18251490.146728112960
3.56-4.070.15491720.126128192991
4.08-5.130.12051700.120228343004
5.13-47.570.14841240.149929633087

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