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- PDB-5ok7: Conservatively refined structure of Gan1D-E170Q, a catalytic muta... -

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Basic information

Entry
Database: PDB / ID: 5ok7
TitleConservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / 6-phospho-beta-galactosidase / Geobacillus stearothermophilus / Glycoside Hydrolase / GH1 family
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 / pdbx_initial_refinement_model
Item: _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
C: Putative 6-phospho-beta-galactobiosidase
D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,14719
Polymers224,8354
Non-polymers1,31215
Water41,7412317
1
A: Putative 6-phospho-beta-galactobiosidase
hetero molecules

D: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0169
Polymers112,4172
Non-polymers5997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area5090 Å2
ΔGint-11 kcal/mol
Surface area32160 Å2
MethodPISA
2
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules

C: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,13110
Polymers112,4172
Non-polymers7148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area4760 Å2
ΔGint-17 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.549, 97.430, 105.249
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 56208.730 Da / Num. of mol.: 4 / Mutation: E170Q
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.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2317 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-19% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 414523 / % possible obs: 91.4 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.8
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / CC1/2: 0.728 / % possible all: 50.8

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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: 4ZEH

4zeh
PDB Unreleased entry


Resolution: 1.34→43.912 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1456 4096 0.99 %
Rwork0.1227 --
obs0.1229 414365 91.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→43.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15174 0 87 2317 17578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616389
X-RAY DIFFRACTIONf_angle_d0.87622399
X-RAY DIFFRACTIONf_dihedral_angle_d19.0296076
X-RAY DIFFRACTIONf_chiral_restr0.082231
X-RAY DIFFRACTIONf_plane_restr0.0062945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.35580.2678860.21147675X-RAY DIFFRACTION50
1.3558-1.37230.2274930.20088421X-RAY DIFFRACTION55
1.3723-1.38970.21631020.18859251X-RAY DIFFRACTION60
1.3897-1.4080.20751050.181110041X-RAY DIFFRACTION65
1.408-1.42720.2168960.171910935X-RAY DIFFRACTION71
1.4272-1.44760.22221090.164811927X-RAY DIFFRACTION77
1.4476-1.46930.21111100.157112875X-RAY DIFFRACTION83
1.4693-1.49220.21381010.141714028X-RAY DIFFRACTION90
1.4922-1.51670.16911740.126115155X-RAY DIFFRACTION98
1.5167-1.54280.14811400.116715462X-RAY DIFFRACTION100
1.5428-1.57090.17411400.109915499X-RAY DIFFRACTION100
1.5709-1.60110.13611410.107915439X-RAY DIFFRACTION100
1.6011-1.63380.13561540.103615412X-RAY DIFFRACTION100
1.6338-1.66930.1441600.105815461X-RAY DIFFRACTION100
1.6693-1.70810.15211500.107215467X-RAY DIFFRACTION100
1.7081-1.75090.13371500.107815485X-RAY DIFFRACTION100
1.7509-1.79820.14891770.108115441X-RAY DIFFRACTION100
1.7982-1.85110.14461870.108315441X-RAY DIFFRACTION100
1.8511-1.91090.14131730.10615510X-RAY DIFFRACTION100
1.9109-1.97920.12261670.106615442X-RAY DIFFRACTION100
1.9792-2.05840.13531310.108815475X-RAY DIFFRACTION100
2.0584-2.15210.13621420.110515518X-RAY DIFFRACTION100
2.1521-2.26550.13541630.114215520X-RAY DIFFRACTION100
2.2655-2.40750.16781600.121715456X-RAY DIFFRACTION100
2.4075-2.59330.15081790.127315513X-RAY DIFFRACTION100
2.5933-2.85430.13871580.129915545X-RAY DIFFRACTION100
2.8543-3.26720.14581650.127915600X-RAY DIFFRACTION100
3.2672-4.11580.1221500.117615584X-RAY DIFFRACTION100
4.1158-43.9360.12941330.136215691X-RAY DIFFRACTION99

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