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- PDB-5oka: Non-conservatively refined structure of Gan1D-E170Q, a catalytic ... -

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Basic information

Entry
Database: PDB / ID: 5oka
TitleNon-conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a 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: 1.25 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
Water41,7052315
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 area32210 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 area4790 Å2
ΔGint-17 kcal/mol
Surface area31970 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.: 2315 / 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, 0.1M 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: 1.25→50 Å / Num. obs: 448160 / % possible obs: 80.2 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5822 / CC1/2: 0.45 / % possible all: 21.1

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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: 4ZEH

4zeh
PDB Unreleased entry


Resolution: 1.25→43.912 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.42
RfactorNum. reflection% reflection
Rfree0.1492 4520 1.01 %
Rwork0.1274 --
obs0.1276 443574 80.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→43.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15174 0 87 2315 17576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516421
X-RAY DIFFRACTIONf_angle_d0.89422450
X-RAY DIFFRACTIONf_dihedral_angle_d19.3896097
X-RAY DIFFRACTIONf_chiral_restr0.082237
X-RAY DIFFRACTIONf_plane_restr0.0062952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.3558400.30343610X-RAY DIFFRACTION20
1.2642-1.27910.3345420.28024627X-RAY DIFFRACTION25
1.2791-1.29470.3046410.26395552X-RAY DIFFRACTION30
1.2947-1.31110.2678660.24126498X-RAY DIFFRACTION35
1.3111-1.32830.3173730.23197551X-RAY DIFFRACTION41
1.3283-1.34650.2065800.20998527X-RAY DIFFRACTION46
1.3465-1.36580.2314810.20349676X-RAY DIFFRACTION52
1.3658-1.38610.2563960.192510639X-RAY DIFFRACTION58
1.3861-1.40780.21791200.178611983X-RAY DIFFRACTION65
1.4078-1.43090.20431530.164813140X-RAY DIFFRACTION72
1.4309-1.45560.19421590.155814430X-RAY DIFFRACTION79
1.4556-1.4820.21061650.14615914X-RAY DIFFRACTION86
1.482-1.51050.18172090.136217585X-RAY DIFFRACTION96
1.5105-1.54140.16551900.1318401X-RAY DIFFRACTION100
1.5414-1.57490.14671590.12818426X-RAY DIFFRACTION100
1.5749-1.61150.14291720.116418424X-RAY DIFFRACTION100
1.6115-1.65180.15671760.109418387X-RAY DIFFRACTION100
1.6518-1.69650.14621920.109618443X-RAY DIFFRACTION100
1.6965-1.74640.1551960.110218369X-RAY DIFFRACTION100
1.7464-1.80280.12161670.110618437X-RAY DIFFRACTION100
1.8028-1.86720.13351920.117118385X-RAY DIFFRACTION100
1.8672-1.9420.13011930.116618478X-RAY DIFFRACTION100
1.942-2.03040.13821550.114918492X-RAY DIFFRACTION100
2.0304-2.13740.13721920.113518403X-RAY DIFFRACTION100
2.1374-2.27130.15242170.113918442X-RAY DIFFRACTION100
2.2713-2.44670.13711720.122918461X-RAY DIFFRACTION100
2.4467-2.69290.13762230.127418477X-RAY DIFFRACTION100
2.6929-3.08240.12932020.128618504X-RAY DIFFRACTION100
3.0824-3.88320.14262160.119418567X-RAY DIFFRACTION100
3.8832-43.93950.1391810.129218621X-RAY DIFFRACTION99

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