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- PDB-5vqd: Beta-glucoside phosphorylase BglX -

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Basic information

Entry
Database: PDB / ID: 5vqd
TitleBeta-glucoside phosphorylase BglX
ComponentsBeta-glucoside phosphorylase BglX
KeywordsHYDROLASE / Beta-glucoside phosphorylase / CAZy family 3 GH3 BglX
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 / Beta-glucoside phosphorylase BglX
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-glucoside phosphorylase BglX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8583
Polymers64,6741
Non-polymers1842
Water8,449469
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)129,7176
Polymers129,3482
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5260 Å2
ΔGint-19 kcal/mol
Surface area36450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.520, 84.150, 161.190
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: 2.1→54.72 Å / Num. obs: 30635 / % possible obs: 94.6 % / Redundancy: 10.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 2647 / CC1/2: 0.975 / % possible all: 99.9

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Processing

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

3bmx


Resolution: 2.1→33.127 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1964 6.5 %Random selection
Rwork0.2045 ---
obs0.208 30206 93.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 12 469 4779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024408
X-RAY DIFFRACTIONf_angle_d0.5655975
X-RAY DIFFRACTIONf_dihedral_angle_d11.6882663
X-RAY DIFFRACTIONf_chiral_restr0.042667
X-RAY DIFFRACTIONf_plane_restr0.003773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.22751580.18072126X-RAY DIFFRACTION100
2.1525-2.21070.29651390.22022119X-RAY DIFFRACTION100
2.2107-2.27580.7047800.54181094X-RAY DIFFRACTION52
2.2758-2.34920.29331490.25092066X-RAY DIFFRACTION97
2.3492-2.43310.29011440.22652152X-RAY DIFFRACTION100
2.4331-2.53050.28571520.20412156X-RAY DIFFRACTION100
2.5305-2.64570.2551490.19862137X-RAY DIFFRACTION100
2.6457-2.78510.25841160.19941810X-RAY DIFFRACTION84
2.7851-2.95950.23081470.19892137X-RAY DIFFRACTION100
2.9595-3.18780.24891580.19682151X-RAY DIFFRACTION100
3.1878-3.50830.24631340.18361981X-RAY DIFFRACTION91
3.5083-4.01520.22831250.19111826X-RAY DIFFRACTION84
4.0152-5.05580.16191510.14012206X-RAY DIFFRACTION100
5.0558-33.13080.20791620.18892281X-RAY DIFFRACTION100

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