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- PDB-6kdc: crystal structure of Fpglu1 from fervidobacterium pennivoraus -

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Basic information

Entry
Database: PDB / ID: 6kdc
Titlecrystal structure of Fpglu1 from fervidobacterium pennivoraus
ComponentsBeta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


beta-glucosidase activity / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...: / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase
Similarity search - Component
Biological speciesFervidobacterium pennivorans DSM 9078 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYu, S. / LiuQing, C.
CitationJournal: To Be Published
Title: crystal structure of fpglu1
Authors: Yu, S.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2708
Polymers54,6921
Non-polymers5787
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.040, 101.397, 170.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-784-

HOH

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Components

#1: Protein Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase


Mass: 54691.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium pennivorans DSM 9078 (bacteria)
Strain: DSM 9078 / Ven5 / Gene: Ferpe_1843 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9UEF1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.989 Å
DetectorType: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 46813 / % possible obs: 100 % / Redundancy: 9.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.106 / Net I/σ(I): 4
Reflection shellResolution: 1.85→1.99 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2715 / CC1/2: 0.985 / Rpim(I) all: 0.132 / Rrim(I) all: 0.507 / Χ2: 1.004

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.18 2401 -
Rwork0.154 --
obs-44408 95 %
Refinement stepCycle: LAST / Resolution: 1.85→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 32 293 4196
LS refinement shellResolution: 1.85→1.91 Å
RfactorNum. reflection% reflection
Rfree0.175 215 -
Rwork0.165 4352 -
obs--99 %

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