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- PDB-8in6: Eisenia hydrolysis-enhancing protein from Aplysia kurodai complex... -

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Basic information

Entry
Database: PDB / ID: 8in6
TitleEisenia hydrolysis-enhancing protein from Aplysia kurodai complex with tannic acid
Components25 kDa polyphenol-binding protein
KeywordsUNKNOWN FUNCTION / protect glucosidase from inhibition
Function / homologyChitin-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 / BETA-1,2,3,4,6-PENTA-O-GALLOYL-D-GLUCOPYRANOSE / 25 kDa polyphenol-binding protein
Function and homology information
Biological speciesAplysia kurodai (Kuroda's sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)25,6112
Polymers24,6701
Non-polymers9411
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-9 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.463, 65.356, 67.173
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-GGP / BETA-1,2,3,4,6-PENTA-O-GALLOYL-D-GLUCOPYRANOSE


Mass: 940.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H32O26 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.89 Å3/Da / Density % sol: 34.89 %
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-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→46.84 Å / Num. obs: 15284 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0821 / Net I/σ(I): 15.39
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.8228 / Num. unique obs: 1493 / CC1/2: 0.737 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.89 Å / SU ML: 0.2654 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 735 4.8 %
Rwork0.1931 14565 -
obs0.1951 15283 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 67 85 1705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811704
X-RAY DIFFRACTIONf_angle_d0.98712350
X-RAY DIFFRACTIONf_chiral_restr0.0605236
X-RAY DIFFRACTIONf_plane_restr0.0079315
X-RAY DIFFRACTIONf_dihedral_angle_d14.9286256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.040.33461490.27322843X-RAY DIFFRACTION99.11
2.05-2.250.28481390.21012865X-RAY DIFFRACTION99.97
2.25-2.580.24941440.20732888X-RAY DIFFRACTION99.97
2.58-3.240.28421520.19492919X-RAY DIFFRACTION99.97
3.25-35.890.1861510.17293050X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: -5.03160430185 Å / Origin y: 6.42106978878 Å / Origin z: -7.63147150499 Å
111213212223313233
T0.19109126038 Å20.00040828970908 Å2-0.0141087318625 Å2-0.181964767737 Å2-0.00742491190468 Å2--0.186905340873 Å2
L1.15456917316 °2-0.22480890798 °20.678294403044 °2-0.732991899738 °20.107190857172 °2--0.554169659366 °2
S0.172350691296 Å °0.054559425561 Å °-0.146353437918 Å °-0.0902071538253 Å °-0.0171152534609 Å °-0.0443471707337 Å °0.17021750361 Å °-0.012511801832 Å °0.00151753021113 Å °
Refinement TLS groupSelection details: all

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