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

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Basic information

Entry
Database: PDB / ID: 5okh
TitleConservatively refined structure of Gan1D-WT, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in the C2 spacegroup
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-beta-phospho-galactosidase / glycoside hydrolase / GH1 / 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
IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)112,7726
Polymers112,4192
Non-polymers3524
Water9,404522
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-3 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.020, 68.810, 152.770
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-951-

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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16-19% PEG8K, 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: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→25.6 Å / Num. obs: 76802 / % possible obs: 99.9 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.9
Reflection shellResolution: 1.98→2.02 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4553 / CC1/2: 0.929 / % possible all: 100

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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: 5OKB

5okb


Resolution: 1.98→25.593 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 3853 5.02 %
Rwork0.1878 --
obs0.19 76752 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→25.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 24 522 8286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078085
X-RAY DIFFRACTIONf_angle_d0.81911013
X-RAY DIFFRACTIONf_dihedral_angle_d15.4044695
X-RAY DIFFRACTIONf_chiral_restr0.0521103
X-RAY DIFFRACTIONf_plane_restr0.0051445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00420.32141460.28062603X-RAY DIFFRACTION100
2.0042-2.02950.3371240.26672539X-RAY DIFFRACTION100
2.0295-2.05620.31371390.27182622X-RAY DIFFRACTION100
2.0562-2.08440.31461340.25812587X-RAY DIFFRACTION100
2.0844-2.11410.32671370.24432560X-RAY DIFFRACTION100
2.1141-2.14570.3451550.23562619X-RAY DIFFRACTION100
2.1457-2.17920.27141360.23982524X-RAY DIFFRACTION100
2.1792-2.21490.33351440.23652635X-RAY DIFFRACTION100
2.2149-2.25310.28921390.24392543X-RAY DIFFRACTION100
2.2531-2.2940.27911380.23292666X-RAY DIFFRACTION100
2.294-2.33810.31271410.22522512X-RAY DIFFRACTION100
2.3381-2.38580.25521300.2182632X-RAY DIFFRACTION100
2.3858-2.43760.2791390.22082589X-RAY DIFFRACTION100
2.4376-2.49430.27021350.20432582X-RAY DIFFRACTION100
2.4943-2.55660.26611430.20812619X-RAY DIFFRACTION100
2.5566-2.62570.2551290.20542578X-RAY DIFFRACTION100
2.6257-2.70280.24921330.20912618X-RAY DIFFRACTION100
2.7028-2.790.26031300.20232623X-RAY DIFFRACTION100
2.79-2.88960.29481340.21052582X-RAY DIFFRACTION100
2.8896-3.00510.25271100.20932647X-RAY DIFFRACTION100
3.0051-3.14160.24661230.20522603X-RAY DIFFRACTION100
3.1416-3.30690.2481490.19732585X-RAY DIFFRACTION100
3.3069-3.51360.22511640.18572611X-RAY DIFFRACTION100
3.5136-3.78410.22271430.16942617X-RAY DIFFRACTION100
3.7841-4.16350.18181450.14942613X-RAY DIFFRACTION100
4.1635-4.76260.15521380.12972620X-RAY DIFFRACTION100
4.7626-5.98770.14841320.13642668X-RAY DIFFRACTION100
5.9877-25.59530.16451430.14022702X-RAY DIFFRACTION99

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