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- PDB-8b80: The structure of Gan1D W433A in complex with galactose-6P -

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Basic information

Entry
Database: PDB / ID: 8b80
TitleThe structure of Gan1D W433A in complex with galactose-6P
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-phospho-beta-galactosidase / galactose-6-phosphate / GH1 / glycoside hydrolase
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
6-O-phosphono-beta-D-galactopyranose / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSnyder, J. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Not funded Israel
CitationJournal: To Be Published
Title: The structure of Gan1D W433A in complex with galactose-6P
Authors: Snyder, J. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 6-phospho-beta-galactobiosidase
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8657
Polymers110,3052
Non-polymers5595
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-4 kcal/mol
Surface area32130 Å2
Unit cell
Length a, b, c (Å)107.500, 68.600, 152.290
Angle α, β, γ (deg.)90.000, 99.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

#1: Protein Putative 6-phospho-beta-galactobiosidase


Mass: 55152.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan1D / Production host: Escherichia coli (E. coli) / References: UniProt: W8QF82, 6-phospho-beta-galactosidase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Sugar ChemComp-BGP / 6-O-phosphono-beta-D-galactopyranose / BETA-GALACTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-galactose / 6-O-phosphono-D-galactose / 6-O-phosphono-galactose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Galp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 19% polyethylene glycol 8 K, 3% MPD, 0.1 M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 104900 / % possible obs: 99.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.97
Reflection shellResolution: 1.78→1.88 Å / Rmerge(I) obs: 0.944 / Num. unique obs: 16376

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKH

5okh


Resolution: 1.78→19.932 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2093 2 %
Rwork0.1784 102729 -
obs0.1792 104822 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.13 Å2 / Biso mean: 38.3736 Å2 / Biso min: 18.68 Å2
Refinement stepCycle: final / Resolution: 1.78→19.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 37 593 8360
Biso mean--39.08 42.52 -
Num. residues----948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.78-1.81730.33591310.3146642593
1.8173-1.86270.3071380.27776779100
1.8627-1.9130.30511400.26316837100
1.913-1.96920.26511400.24656843100
1.9692-2.03270.24491370.22476859100
2.0327-2.10530.281380.21696822100
2.1053-2.18950.2541410.21766909100
2.1895-2.2890.28481390.20396834100
2.289-2.40950.25171400.20526855100
2.4095-2.56020.25121410.19716913100
2.5602-2.75740.23681410.19226890100
2.7574-3.0340.21711400.18746873100
3.034-3.4710.20441410.17326896100
3.471-4.36560.17921410.1456919100
4.3656-19.9320.16711450.13717075100

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