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- PDB-5okr: Conservatively refined structure of Gan1D-WT, a putative 6-phosph... -

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Basic information

Entry
Database: PDB / ID: 5okr
TitleConservatively refined structure of Gan1D-WT, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-beta-glucose
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-phospho-beta-glucose / 6-phospho-beta-galactose / GH1 / glycoside hydrolase / Gan1D
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate catabolic process / beta-glucosidase activity / cytosol
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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
CitationJournal: FEBS J. / Year: 2017
Title: Structural basis for enzyme bifunctionality - the case of Gan1D from Geobacillus stearothermophilus.
Authors: Lansky, S. / Zehavi, A. / Belrhali, H. / Shoham, Y. / Shoham, G.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 2024Group: 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

Downloads & links

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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)113,3779
Polymers112,4192
Non-polymers9587
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-20 kcal/mol
Surface area32390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.260, 68.950, 153.010
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-915-

HOH

21A-960-

HOH

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Components

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


Mass: 56209.715 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: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-19% PEG 8K, 3% MPD, 0.1M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→27.88 Å / Num. obs: 58841 / % possible obs: 98.1 % / Redundancy: 3.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.9
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2 / Num. unique obs: 12183 / CC1/2: 0.839 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKH

5okh


Resolution: 2.15→27.88 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.09
RfactorNum. reflection% reflection
Rfree0.2153 2978 5.06 %
Rwork0.1661 --
obs0.1686 55863 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 61 547 8356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078062
X-RAY DIFFRACTIONf_angle_d0.84110970
X-RAY DIFFRACTIONf_dihedral_angle_d15.3634633
X-RAY DIFFRACTIONf_chiral_restr0.0511102
X-RAY DIFFRACTIONf_plane_restr0.0061430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18530.33531310.25792394X-RAY DIFFRACTION90
2.1853-2.22290.27831420.22342494X-RAY DIFFRACTION93
2.2229-2.26340.26581530.21852539X-RAY DIFFRACTION95
2.2634-2.30690.25551240.20442577X-RAY DIFFRACTION95
2.3069-2.35390.26561270.20872645X-RAY DIFFRACTION97
2.3539-2.40510.23191300.19322592X-RAY DIFFRACTION97
2.4051-2.4610.26211330.19472652X-RAY DIFFRACTION97
2.461-2.52250.24841550.18692611X-RAY DIFFRACTION98
2.5225-2.59070.29741390.18412651X-RAY DIFFRACTION99
2.5907-2.66680.24061260.1862736X-RAY DIFFRACTION100
2.6668-2.75280.23831450.17552711X-RAY DIFFRACTION100
2.7528-2.85110.23941410.17762687X-RAY DIFFRACTION100
2.8511-2.96520.23671500.18022674X-RAY DIFFRACTION100
2.9652-3.10.25371370.17952709X-RAY DIFFRACTION100
3.1-3.26320.22751360.17112735X-RAY DIFFRACTION100
3.2632-3.46720.20851610.16552700X-RAY DIFFRACTION100
3.4672-3.73440.21521340.15052748X-RAY DIFFRACTION100
3.7344-4.10910.16471590.13372693X-RAY DIFFRACTION100
4.1091-4.70130.1611660.11832717X-RAY DIFFRACTION100
4.7013-5.91380.15021370.13262765X-RAY DIFFRACTION100
5.9138-27.88210.17671520.14322810X-RAY DIFFRACTION100

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