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- PDB-9kr2: Structural Basis for the Polymer-Protein Binding Mechanism of Pol... -

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Basic information

Entry
Database: PDB / ID: 9kr2
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: / ACETATE ION / PHOSPHATE ION
Function and homology information
Biological speciesComamonas sp. NyZ500 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)43,1826
Polymers42,5161
Non-polymers6675
Water9,188510
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)164.739, 164.739, 164.739
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-808-

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 , 5 types, 515 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-A1EGH / [(3S,5S,7S,9R,11S,13S)-1,3,7,9,11,13,15-heptakis(oxidanyl)pentadecan-5-yl] ethanoate


Mass: 382.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 71.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.8 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 5.0

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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: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→82.37 Å / Num. obs: 41614 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.197 / Net I/σ(I): 12.9
Reflection shellResolution: 2.13→2.19 Å / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3351 / CC1/2: 0.91 / Rpim(I) all: 0.286

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→44.03 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 2088 5.03 %
Rwork0.154 39448 -
obs0.1554 41536 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.17 Å2 / Biso mean: 23.8904 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 2.13→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 41 510 3447
Biso mean--52.35 34.65 -
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.13-2.180.22591450.179826162761
2.18-2.230.23621450.182425962741
2.23-2.30.25391390.196926022741
2.3-2.360.19171460.156926082754
2.36-2.440.21991360.167425862722
2.44-2.530.23721220.164326582780
2.53-2.630.19491390.165325972736
2.63-2.750.19351330.17126352768
2.75-2.890.21761280.172526332761
2.89-3.070.18381610.162225832744
3.07-3.310.17381290.1626482777
3.31-3.640.20181310.148326562787
3.65-4.170.14841330.123626472780
4.17-5.250.13421470.122626642811
5.26-44.030.14861540.150227192873

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