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- PDB-5vqe: Beta-glucoside phosphorylase BglX bound to 2FGlc -

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Basic information

Entry
Database: PDB / ID: 5vqe
TitleBeta-glucoside phosphorylase BglX bound to 2FGlc
ComponentsBeta-glucoside phosphorylase BglX
KeywordsHYDROLASE / Beta-glucoside phosphorylase / CAZy family 3 GH3 BglX 2FGlc 2 / 4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
Function / homologyGlycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / 2-deoxy-2-fluoro-alpha-D-glucopyranose / Beta-glucoside phosphorylase BglX
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.889 Å
AuthorsPatel, A. / Mark, B.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and mechanistic analysis of a beta-glycoside phosphorylase identified by screening a metagenomic library.
Authors: Macdonald, S.S. / Patel, A. / Larmour, V.L.C. / Morgan-Lang, C. / Hallam, S.J. / Mark, B.L. / Withers, S.G.
History
DepositionMay 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-glucoside phosphorylase BglX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8562
Polymers64,6741
Non-polymers1821
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-glucoside phosphorylase BglX
hetero molecules

A: Beta-glucoside phosphorylase BglX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,7134
Polymers129,3482
Non-polymers3642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4300 Å2
ΔGint-8 kcal/mol
Surface area37530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.390, 83.950, 161.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-glucoside phosphorylase BglX


Mass: 64674.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFS5*PLUS
#2: Sugar ChemComp-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 27% PEG 1000 and 100 mM MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→54.63 Å / Num. obs: 43306 / % possible obs: 98.4 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 2693 / CC1/2: 0.958 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
AimlessCCP4 7.0data scaling
PHENIXdev_2481phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMX (Sculptor edited)

3bmx


Resolution: 1.889→33.117 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 1996 4.62 %
Rwork0.1725 --
obs0.1741 43226 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.889→33.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 11 366 4704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054442
X-RAY DIFFRACTIONf_angle_d0.8166027
X-RAY DIFFRACTIONf_dihedral_angle_d12.482683
X-RAY DIFFRACTIONf_chiral_restr0.05673
X-RAY DIFFRACTIONf_plane_restr0.005780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.889-1.93630.29231440.28252856X-RAY DIFFRACTION95
1.9363-1.98860.24291270.19462844X-RAY DIFFRACTION97
1.9886-2.04710.19531350.17012898X-RAY DIFFRACTION97
2.0471-2.11320.23471480.16252882X-RAY DIFFRACTION97
2.1132-2.18870.21921300.172893X-RAY DIFFRACTION97
2.1887-2.27630.28661440.24182879X-RAY DIFFRACTION96
2.2763-2.37990.22561470.18482881X-RAY DIFFRACTION97
2.3799-2.50530.22581450.18022966X-RAY DIFFRACTION98
2.5053-2.66220.19271390.1642948X-RAY DIFFRACTION99
2.6622-2.86760.19031390.16782980X-RAY DIFFRACTION99
2.8676-3.1560.19771480.17172983X-RAY DIFFRACTION99
3.156-3.61220.20351480.16593015X-RAY DIFFRACTION99
3.6122-4.54920.16551450.13723042X-RAY DIFFRACTION100
4.5492-33.12160.18441570.16363163X-RAY DIFFRACTION100

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