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- PDB-5okq: Non-conservatively refined structure of Gan1D-WT, a putative 6-ph... -

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Basic information

Entry
Database: PDB / ID: 5okq
TitleNon-conservatively 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 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-galactopyranose / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-8 kcal/mol
Surface area31520 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-899-

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


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


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


Mass: 18.015 Da / Num. of mol.: 479 / 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: 1.85→31.2 Å / Num. obs: 92547 / % possible obs: 98.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.2
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3850 / CC1/2: 0.564 / % possible all: 84.1

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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: 1.85→30.53 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.215 4642 5.02 %
Rwork0.1834 --
obs0.1851 87886 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7745 0 112 479 8336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078111
X-RAY DIFFRACTIONf_angle_d0.84511023
X-RAY DIFFRACTIONf_dihedral_angle_d15.6784651
X-RAY DIFFRACTIONf_chiral_restr0.0531104
X-RAY DIFFRACTIONf_plane_restr0.0051435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.37921560.3912414X-RAY DIFFRACTION82
1.871-1.8930.40961260.35092566X-RAY DIFFRACTION89
1.893-1.91610.31361510.30652777X-RAY DIFFRACTION93
1.9161-1.94040.32061530.29062892X-RAY DIFFRACTION98
1.9404-1.96590.28711310.26312969X-RAY DIFFRACTION100
1.9659-1.99280.29411610.2422991X-RAY DIFFRACTION100
1.9928-2.02130.26791350.23072927X-RAY DIFFRACTION100
2.0213-2.05150.27661470.2292964X-RAY DIFFRACTION100
2.0515-2.08350.26751380.22342935X-RAY DIFFRACTION100
2.0835-2.11770.25391560.21552980X-RAY DIFFRACTION100
2.1177-2.15420.24741480.21692938X-RAY DIFFRACTION100
2.1542-2.19330.27731500.21823003X-RAY DIFFRACTION100
2.1933-2.23550.25931880.20132861X-RAY DIFFRACTION100
2.2355-2.28110.21481460.18913017X-RAY DIFFRACTION100
2.2811-2.33070.23631860.19682886X-RAY DIFFRACTION100
2.3307-2.38490.23751430.19562969X-RAY DIFFRACTION100
2.3849-2.44450.30811520.19853005X-RAY DIFFRACTION100
2.4445-2.51060.23821710.1852917X-RAY DIFFRACTION100
2.5106-2.58440.22061300.19182967X-RAY DIFFRACTION100
2.5844-2.66780.23821570.18842969X-RAY DIFFRACTION100
2.6678-2.76310.21331730.18472990X-RAY DIFFRACTION100
2.7631-2.87360.21391480.17982945X-RAY DIFFRACTION100
2.8736-3.00430.20791670.17012966X-RAY DIFFRACTION100
3.0043-3.16250.18621720.16432977X-RAY DIFFRACTION100
3.1625-3.36040.18251620.1662961X-RAY DIFFRACTION100
3.3604-3.61950.20121710.15762958X-RAY DIFFRACTION100
3.6195-3.98310.17061640.15143000X-RAY DIFFRACTION100
3.9831-4.55780.17171500.14333005X-RAY DIFFRACTION100
4.5578-5.73610.18561630.16493005X-RAY DIFFRACTION100
5.7361-30.5340.17931470.17243093X-RAY DIFFRACTION100

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