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- PDB-8ysv: Crystal structure of beta - glucosidase 6PG from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 8ysv
TitleCrystal structure of beta - glucosidase 6PG from Enterococcus faecalis
Components6-phospho-beta-glucosidase
KeywordsHYDROLASE / Glycoside hydrolase families / Degrade glucose
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ETHANOL / NICKEL (II) ION / 6-phospho-beta-glucosidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWang, W.Y. / Li, Y.J. / Liu, Z.Y. / Han, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2019GG007 China
CitationJournal: To Be Published
Title: Crystal structure of beta - glucosidase 6PG from Enterococcus faecalis
Authors: Wang, W.Y. / Li, Y.J. / Liu, Z.Y. / Han, X.D.
History
DepositionMar 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1028
Polymers54,6971
Non-polymers4057
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: No ligand
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 6-phospho-beta-glucosidase
hetero molecules

A: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,20516
Polymers109,3952
Non-polymers81014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5840 Å2
ΔGint-115 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.110, 79.000, 58.080
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-505-

NI

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-phospho-beta-glucosidase


Mass: 54697.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EY666_00860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q1FR04

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Non-polymers , 6 types, 236 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.86 Å3/Da / Density % sol: 37.8 % / Description: virgate crystal
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Ammonium sulfate,HEPES pH7.0 / PH range: 5.5-9.0

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.79→42.22 Å / Num. obs: 40049 / % possible obs: 99.7 % / Redundancy: 6.68 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 11.4
Reflection shellResolution: 1.79→1.84 Å / Rmerge(I) obs: 1.781 / Num. unique obs: 2937 / CC1/2: 0.529

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f66

4f66


Resolution: 1.79→30.278 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2055 5.13 %RANDOM
Rwork0.1873 ---
obs0.1895 40037 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→30.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 13 229 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064001
X-RAY DIFFRACTIONf_angle_d0.8375423
X-RAY DIFFRACTIONf_dihedral_angle_d6.2423229
X-RAY DIFFRACTIONf_chiral_restr0.054547
X-RAY DIFFRACTIONf_plane_restr0.006709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83170.36221340.31212478X-RAY DIFFRACTION99
1.8317-1.87750.32031460.26292524X-RAY DIFFRACTION99
1.8775-1.92820.27191540.24312512X-RAY DIFFRACTION100
1.9282-1.98490.27491350.23722505X-RAY DIFFRACTION100
1.9849-2.0490.26551350.22512543X-RAY DIFFRACTION99
2.049-2.12220.27851410.20592489X-RAY DIFFRACTION100
2.1222-2.20720.26671340.19932528X-RAY DIFFRACTION100
2.2072-2.30760.24151200.19692572X-RAY DIFFRACTION100
2.3076-2.42920.24381160.19742560X-RAY DIFFRACTION100
2.4292-2.58130.25441660.19492478X-RAY DIFFRACTION100
2.5813-2.78050.24661400.1912553X-RAY DIFFRACTION100
2.7805-3.06010.24591380.1922559X-RAY DIFFRACTION100
3.0601-3.50230.22041370.19182544X-RAY DIFFRACTION100
3.5023-4.41030.1641190.14262558X-RAY DIFFRACTION100
4.4103-30.2750.18221400.15532579X-RAY DIFFRACTION99

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