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- PDB-8b81: The structure of Gan1D W433A in complex with cellobiose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 8b81
TitleThe structure of Gan1D W433A in complex with cellobiose-6-phosphate
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / glycoside hydrolase / GH1 / cellobiose-6-phosphate / 6-phospho-beta-glucosidase
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
beta-cellobiose-6-phosphate / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.585 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 cellobiose-6-phosphate
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)111,4268
Polymers110,3052
Non-polymers1,1216
Water17,835990
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-2 kcal/mol
Surface area31500 Å2
Unit cell
Length a, b, c (Å)107.900, 68.380, 149.800
Angle α, β, γ (deg.)90.000, 99.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

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: Polysaccharide 6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1b_1-5_6*OPO/3O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% polyethylene glycol 8K, 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-F / 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: 1.585→50 Å / Num. obs: 141155 / % possible obs: 96.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7
Reflection shellResolution: 1.585→1.68 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 20970 / % possible all: 89.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B80

8b80


Resolution: 1.585→49.269 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 2816 2 %
Rwork0.1691 138146 -
obs0.1697 140962 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.02 Å2 / Biso mean: 27.5809 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.585→49.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 74 990 8794
Biso mean--35.8 36.97 -
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 (%)
1.5855-1.61280.37071030.3707503671
1.6128-1.64210.33341410.299688797
1.6421-1.67370.28831400.2614688897
1.6737-1.70790.26381420.238691097
1.7079-1.7450.27441400.2226689798
1.745-1.78560.29441410.2084695898
1.7856-1.83030.2411410.1994698798
1.8303-1.87980.22751420.1998693598
1.8798-1.93510.23921430.1948700498
1.9351-1.99750.23161420.185695998
1.9975-2.06890.20421400.1778691897
2.0689-2.15180.18641430.1729698498
2.1518-2.24970.20411430.1699702599
2.2497-2.36830.22471440.1725701998
2.3683-2.51670.18931430.1636704699
2.5167-2.7110.19111450.1626708099
2.711-2.98380.17131450.1645711399
2.9838-3.41540.22171440.1713706498
3.4154-4.30270.191450.145713599
4.3027-49.2690.14881490.1338730199

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