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- PDB-8in3: Eisenia hydrolysis-enhancing protein from Aplysia kurodai -

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Basic information

Entry
Database: PDB / ID: 8in3
TitleEisenia hydrolysis-enhancing protein from Aplysia kurodai
Components25 kDa polyphenol-binding protein
KeywordsUNKNOWN FUNCTION / EHEP
Function / homology: / Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / chitin binding / extracellular region / 25 kDa polyphenol-binding protein
Function and homology information
Biological speciesAplysia kurodai (Kuroda's sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsSun, X.M. / Ye, Y.X. / Kato, K. / Yu, J. / Yao, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H01754 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101083 Japan
CitationJournal: Elife / Year: 2023
Title: Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Authors: Sun, X. / Ye, Y. / Sakurai, N. / Wang, H. / Kato, K. / Yu, J. / Yuasa, K. / Tsuji, A. / Yao, M.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: 25 kDa polyphenol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8543
Polymers24,6701
Non-polymers1842
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 65.330, 66.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 25 kDa polyphenol-binding protein


Mass: 24669.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: A0A1B4XTR1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.86 Å3/Da / Density % sol: 33.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0 M sodium acetate, 0.1 M imidazole (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 60994 / % possible obs: 93.41 % / Redundancy: 6.6 % / Biso Wilson estimate: 8.81 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.28
Reflection shellResolution: 1.15→1.195 Å / Num. unique obs: 4888 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→35.62 Å / SU ML: 0.1373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.0217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 2908 4.77 %
Rwork0.182 58079 -
obs0.1823 60987 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.04 Å2
Refinement stepCycle: LAST / Resolution: 1.15→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 12 343 1920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531664
X-RAY DIFFRACTIONf_angle_d0.84062288
X-RAY DIFFRACTIONf_chiral_restr0.0806237
X-RAY DIFFRACTIONf_plane_restr0.0059310
X-RAY DIFFRACTIONf_dihedral_angle_d12.7269584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.4117990.41761916X-RAY DIFFRACTION65.38
1.17-1.190.36861150.36242476X-RAY DIFFRACTION84.73
1.19-1.220.29521400.3172685X-RAY DIFFRACTION92.23
1.22-1.240.28071300.28492691X-RAY DIFFRACTION92.13
1.24-1.260.25081370.24362726X-RAY DIFFRACTION93.29
1.26-1.290.18521400.21182726X-RAY DIFFRACTION92.9
1.29-1.320.21871350.21752744X-RAY DIFFRACTION93.57
1.32-1.350.23021390.22482743X-RAY DIFFRACTION93.54
1.35-1.390.24311390.22882766X-RAY DIFFRACTION94.38
1.39-1.430.22521390.20042780X-RAY DIFFRACTION95.08
1.43-1.480.1641420.17662779X-RAY DIFFRACTION94.56
1.48-1.530.19441410.16972794X-RAY DIFFRACTION95.05
1.53-1.590.1831400.16672830X-RAY DIFFRACTION95.59
1.59-1.660.16581440.16332824X-RAY DIFFRACTION95.93
1.66-1.750.18191390.15792820X-RAY DIFFRACTION94.93
1.75-1.860.17521440.16922885X-RAY DIFFRACTION97.3
1.86-2.010.17371440.15732879X-RAY DIFFRACTION96.55
2.01-2.210.17491470.16042915X-RAY DIFFRACTION97.92
2.21-2.530.17791440.16762950X-RAY DIFFRACTION98.13
2.53-3.180.17361580.1752993X-RAY DIFFRACTION98.5
3.18-35.620.15931520.15663157X-RAY DIFFRACTION99.01

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