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

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Basic information

Entry
Database: PDB / ID: 5okj
TitleNon-conservatively 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-phospho-beta-galactosidase / cellobiose-6-phosphate / glycoside hydrolase / GH1
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 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: 1.76 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7726
Polymers112,4192
Non-polymers3524
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-4 kcal/mol
Surface area32750 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-952-

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.: 520 / 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
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: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.76→25.6 Å / Num. obs: 99264 / % possible obs: 90.8 % / Redundancy: 3.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.7
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2346 / CC1/2: 0.682 / % possible all: 43.4

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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: 1.76→25.593 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.2406 4975 5.01 %
Rwork0.2027 --
obs0.2046 94282 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→25.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 24 520 8280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078085
X-RAY DIFFRACTIONf_angle_d0.83211013
X-RAY DIFFRACTIONf_dihedral_angle_d15.6494695
X-RAY DIFFRACTIONf_chiral_restr0.0531103
X-RAY DIFFRACTIONf_plane_restr0.0051445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.3534680.40361460X-RAY DIFFRACTION42
1.78-1.80090.3693770.36691686X-RAY DIFFRACTION49
1.8009-1.82290.4215960.36441869X-RAY DIFFRACTION54
1.8229-1.8460.33391330.33092030X-RAY DIFFRACTION61
1.846-1.87020.34711220.31492352X-RAY DIFFRACTION68
1.8702-1.89590.36571460.31742541X-RAY DIFFRACTION75
1.8959-1.92290.34491570.30562903X-RAY DIFFRACTION84
1.9229-1.95160.33021760.30693264X-RAY DIFFRACTION95
1.9516-1.98210.40661960.29713394X-RAY DIFFRACTION100
1.9821-2.01460.31281930.26853437X-RAY DIFFRACTION100
2.0146-2.04930.29511910.26773436X-RAY DIFFRACTION100
2.0493-2.08660.32321790.25653432X-RAY DIFFRACTION100
2.0866-2.12670.25691680.24543474X-RAY DIFFRACTION100
2.1267-2.17010.30281530.24363448X-RAY DIFFRACTION100
2.1701-2.21720.31421940.23543442X-RAY DIFFRACTION100
2.2172-2.26880.28441700.23583467X-RAY DIFFRACTION100
2.2688-2.32550.2521620.2313436X-RAY DIFFRACTION100
2.3255-2.38830.27911840.22753477X-RAY DIFFRACTION100
2.3883-2.45850.28181780.22693475X-RAY DIFFRACTION100
2.4585-2.53780.25071990.2183405X-RAY DIFFRACTION100
2.5378-2.62840.27841620.22843454X-RAY DIFFRACTION100
2.6284-2.73360.28851970.22263450X-RAY DIFFRACTION100
2.7336-2.85780.25541790.2243460X-RAY DIFFRACTION100
2.8578-3.00830.25681850.22153459X-RAY DIFFRACTION100
3.0083-3.19640.25291840.21363465X-RAY DIFFRACTION100
3.1964-3.44270.23562000.19343445X-RAY DIFFRACTION100
3.4427-3.78810.21881880.17343479X-RAY DIFFRACTION100
3.7881-4.3340.1691870.14313497X-RAY DIFFRACTION100
4.334-5.45170.1571880.13133489X-RAY DIFFRACTION100
5.4517-25.59580.15611630.14183607X-RAY DIFFRACTION100

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