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- PDB-7eka: crystal structure of epigallocatechin binding with alpha-lactalbumin -

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Basic information

Entry
Database: PDB / ID: 7eka
Titlecrystal structure of epigallocatechin binding with alpha-lactalbumin
ComponentsAlpha-lactalbumin
KeywordsLIGASE / alpha-lactalbumin / epigallocatechin
Function / homology
Function and homology information


response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding ...response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / extracellular space / identical protein binding
Similarity search - Function
Lactalbumin / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL / Alpha-lactalbumin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMa, J. / Yao, Q. / Chen, X. / Zang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Weak Binding of Epigallocatechin to alpha-Lactalbumin Greatly Improves Its Stability and Uptake by Caco-2 Cells.
Authors: Ma, J. / Yao, Q. / Chen, X. / Lv, C. / Zang, J. / Zhao, G.
History
DepositionApr 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2662
Polymers13,9601
Non-polymers3061
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-3 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.344, 69.344, 59.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein Alpha-lactalbumin / Lactose synthase B protein


Mass: 13959.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LALBA, ALACTA / Production host: Bos taurus (cattle) / References: UniProt: P00711
#2: Chemical ChemComp-EGT / 2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL / EPIGALLOCATECHIN


Mass: 306.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 2000 mM ammonium sulfate, 100 mM sodium citrate buffer (pH 5.5)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: May 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.2→40 Å / Num. obs: 50847 / % possible obs: 94.3 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071 / Χ2: 2.191 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.37-1.48.20.2214950.9670.0810.2351.73683.9
1.4-1.439.70.20918020.9770.0710.2211.885100
1.43-1.459.70.19418070.9790.0660.2052.008100
1.45-1.499.60.18517880.9810.0640.1962.086100
1.49-1.529.40.16617870.9850.0580.1762.267100
1.52-1.568.90.16217880.9840.0580.1722.376100
1.56-1.69.20.14217890.9890.050.1512.351100
1.6-1.659.80.13217940.990.0450.1392.383100
1.65-1.79.80.12318190.990.0420.132.345100
1.7-1.769.60.11317810.9930.0390.1192.419100
1.76-1.839.10.10517910.9930.0370.1112.418100
1.83-1.929.30.09618080.9930.0330.1022.504100
1.92-2.02100.08617870.9950.0290.0912.51100
2.02-2.14100.07917940.9960.0260.0842.422100
2.14-2.319.60.07318160.9970.0250.0782.383100
2.31-2.549.70.06318070.9970.0210.0672.036100
2.54-2.9110.30.05718110.9980.0190.061.804100
2.91-3.669.50.05118340.9980.0170.0541.888100
3.66-409.90.04818520.9980.0160.0511.75999.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data collection
HKL-30003.27data scaling
PHENIXmodel building
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ALC

1alc


Resolution: 1.2→21.21 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1763 1999 3.93 %
Rwork0.1683 --
obs0.1686 50846 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→21.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 22 185 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081019
X-RAY DIFFRACTIONf_angle_d1.8481383
X-RAY DIFFRACTIONf_dihedral_angle_d6.71125
X-RAY DIFFRACTIONf_chiral_restr0.095154
X-RAY DIFFRACTIONf_plane_restr0.012173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.2251410.20523475X-RAY DIFFRACTION100
1.23-1.260.22811410.19863497X-RAY DIFFRACTION100
1.26-1.30.18471400.18373476X-RAY DIFFRACTION100
1.3-1.340.21571410.17943456X-RAY DIFFRACTION100
1.34-1.390.18631390.17653476X-RAY DIFFRACTION100
1.39-1.450.18361430.17563483X-RAY DIFFRACTION100
1.45-1.510.1981480.17063459X-RAY DIFFRACTION100
1.51-1.590.1711460.16813465X-RAY DIFFRACTION100
1.59-1.690.18351440.16713524X-RAY DIFFRACTION100
1.69-1.820.18671410.17173480X-RAY DIFFRACTION100
1.82-20.181430.17123479X-RAY DIFFRACTION100
2.01-2.290.18111480.16023508X-RAY DIFFRACTION100
2.3-2.890.16481440.16753497X-RAY DIFFRACTION100
2.89-21.210.1571400.15993572X-RAY DIFFRACTION100

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