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

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Basic information

Entry
Database: PDB / ID: 5okk
TitleConservatively refined structure of Gan1D-WT, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-beta-galactose
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-phospho-beta-galactosidase / 6-phospho-beta-galactose / GH1 / glycoside hydrolase / Gan1D
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
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 / MOLECULAR REPLACEMENT / Resolution: 2.02 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 / pdbx_struct_special_symmetry / 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)114,13718
Polymers112,4192
Non-polymers1,71816
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-7 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.260, 68.520, 153.060
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-898-

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-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.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Galp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


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


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
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: 2.02→31.2 Å / Num. obs: 72119 / % possible obs: 100 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.7
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / CC1/2: 0.893 / % possible all: 99.9

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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: 5OKJ

5okj


Resolution: 2.02→30.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.2106 3638 5.05 %
Rwork0.1685 --
obs0.1706 68471 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 112 481 8341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078111
X-RAY DIFFRACTIONf_angle_d0.84311023
X-RAY DIFFRACTIONf_dihedral_angle_d15.1394651
X-RAY DIFFRACTIONf_chiral_restr0.0521104
X-RAY DIFFRACTIONf_plane_restr0.0051435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.04660.27631470.2382605X-RAY DIFFRACTION100
2.0466-2.07460.2231300.22152598X-RAY DIFFRACTION100
2.0746-2.10430.27421350.2152623X-RAY DIFFRACTION100
2.1043-2.13570.26311410.20412644X-RAY DIFFRACTION100
2.1357-2.1690.26721390.20392556X-RAY DIFFRACTION100
2.169-2.20460.23551490.1972659X-RAY DIFFRACTION100
2.2046-2.24260.22921240.19122599X-RAY DIFFRACTION100
2.2426-2.28330.24151620.18832635X-RAY DIFFRACTION100
2.2833-2.32720.25811430.19732577X-RAY DIFFRACTION100
2.3272-2.37470.26071420.19762642X-RAY DIFFRACTION100
2.3747-2.42630.24921360.19452625X-RAY DIFFRACTION100
2.4263-2.48280.21581340.18812593X-RAY DIFFRACTION100
2.4828-2.54480.22781380.18122685X-RAY DIFFRACTION100
2.5448-2.61360.23691500.18432587X-RAY DIFFRACTION100
2.6136-2.69050.24881380.18582612X-RAY DIFFRACTION100
2.6905-2.77720.20341430.17242638X-RAY DIFFRACTION100
2.7772-2.87640.22871440.16942632X-RAY DIFFRACTION100
2.8764-2.99150.19561560.15712627X-RAY DIFFRACTION100
2.9915-3.12750.20541370.1522610X-RAY DIFFRACTION100
3.1275-3.29220.17541460.15492624X-RAY DIFFRACTION100
3.2922-3.49820.19591320.1542661X-RAY DIFFRACTION100
3.4982-3.76790.18041400.14822650X-RAY DIFFRACTION100
3.7679-4.14620.19161430.142642X-RAY DIFFRACTION100
4.1462-4.74430.18631160.14052670X-RAY DIFFRACTION100
4.7443-5.96990.19051370.17052693X-RAY DIFFRACTION100
5.9699-30.53330.19521360.17022753X-RAY DIFFRACTION100

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