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- PDB-5oks: Non-conservatively refined structure of Gan1D, a 6-phospho-beta-g... -

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Basic information

Entry
Database: PDB / ID: 5oks
TitleNon-conservatively refined structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-beta-glucose
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-phospho-beta-galactosidase / GH1 / glycoside hydrolase / 6-phospho-beta-glucose
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 signature. / Glycosyl hydrolases family 1, N-terminal conserved site / 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 (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 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

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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
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-20 kcal/mol
Surface area32200 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-921-

HOH

21A-962-

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 (unknown)
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


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 / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 546 / 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, 0.1M imidazole buffer pH 6.5, 3% MPD

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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: 1.96→27.88 Å / Num. obs: 70701 / % possible obs: 89.6 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.118 / Net I/σ(I): 6
Reflection shellResolution: 1.96→2 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1 / Num. unique obs: 2275 / CC1/2: 0.503 / % possible all: 45.6

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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
Resolution: 1.96→27.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2168 3541 5.01 %
Rwork0.1808 --
obs0.1826 67156 89.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7745 0 61 546 8352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078062
X-RAY DIFFRACTIONf_angle_d0.85510970
X-RAY DIFFRACTIONf_dihedral_angle_d15.574633
X-RAY DIFFRACTIONf_chiral_restr0.0531102
X-RAY DIFFRACTIONf_plane_restr0.0061430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98690.3867590.35311280X-RAY DIFFRACTION43
1.9869-2.01520.3274620.30321498X-RAY DIFFRACTION50
2.0152-2.04530.3865810.29181709X-RAY DIFFRACTION57
2.0453-2.07730.28711010.28151948X-RAY DIFFRACTION66
2.0773-2.11130.25311130.26532236X-RAY DIFFRACTION75
2.1113-2.14770.31631400.23922473X-RAY DIFFRACTION82
2.1477-2.18670.32141500.24012631X-RAY DIFFRACTION89
2.1867-2.22880.28221370.21422779X-RAY DIFFRACTION93
2.2288-2.27430.24141570.21232867X-RAY DIFFRACTION95
2.2743-2.32370.29361510.20672848X-RAY DIFFRACTION96
2.3237-2.37770.24431430.20542939X-RAY DIFFRACTION97
2.3777-2.43710.23431350.20332890X-RAY DIFFRACTION97
2.4371-2.5030.21841510.20732902X-RAY DIFFRACTION98
2.503-2.57660.27461530.19792970X-RAY DIFFRACTION99
2.5766-2.65970.26181650.19933007X-RAY DIFFRACTION100
2.6597-2.75470.23741680.19232967X-RAY DIFFRACTION100
2.7547-2.86490.22321520.19182984X-RAY DIFFRACTION100
2.8649-2.99510.22571610.1963021X-RAY DIFFRACTION100
2.9951-3.15280.24271520.18323006X-RAY DIFFRACTION100
3.1528-3.350.20691530.17333021X-RAY DIFFRACTION100
3.35-3.60820.19261800.1612963X-RAY DIFFRACTION100
3.6082-3.97040.16831550.14233048X-RAY DIFFRACTION100
3.9704-4.54280.15521670.12483021X-RAY DIFFRACTION100
4.5428-5.71530.15421970.12783003X-RAY DIFFRACTION100
5.7153-27.88250.16711580.14473115X-RAY DIFFRACTION100

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