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

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Basic information

Entry
Database: PDB / ID: 5okg
TitleNon-conservatively refined structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with cellobiose-6-phosphate
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
beta-cellobiose-6-phosphate / 6-O-phosphono-beta-D-glucopyranose / 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 1.4Dec 6, 2017Group: Database references / Category: pdbx_database_related
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)227,51223
Polymers224,8354
Non-polymers2,67719
Water39,3992187
1
A: Putative 6-phospho-beta-galactobiosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)113,79112
Polymers112,4172
Non-polymers1,37310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area5680 Å2
ΔGint-16 kcal/mol
Surface area31710 Å2
MethodPISA
2
C: Putative 6-phospho-beta-galactobiosidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)113,72211
Polymers112,4172
Non-polymers1,3049
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area5230 Å2
ΔGint-22 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.599, 97.480, 105.269
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose-6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1b_1-5_6*OPO/3O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 2202 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2187 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
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 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→36.14 Å / Num. obs: 538379 / % possible obs: 96.3 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.313 / Num. unique obs: 19928 / CC1/2: 0.425 / % possible all: 72.5

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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: 5OK7

5ok7


Resolution: 1.25→36.138 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1583 5417 1.01 %
Rwork0.1389 --
obs0.1391 538256 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→36.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15180 0 173 2187 17540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516462
X-RAY DIFFRACTIONf_angle_d0.93322509
X-RAY DIFFRACTIONf_dihedral_angle_d19.7616144
X-RAY DIFFRACTIONf_chiral_restr0.0812257
X-RAY DIFFRACTIONf_plane_restr0.0062943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.33231240.280712921X-RAY DIFFRACTION70
1.2642-1.27910.25761320.262814325X-RAY DIFFRACTION77
1.2791-1.29470.27711320.241515871X-RAY DIFFRACTION86
1.2947-1.31110.24021800.22317468X-RAY DIFFRACTION95
1.3111-1.32830.23891690.202717851X-RAY DIFFRACTION97
1.3283-1.34650.21961880.193317720X-RAY DIFFRACTION97
1.3465-1.36580.20941740.183917907X-RAY DIFFRACTION97
1.3658-1.38610.18211850.177717830X-RAY DIFFRACTION97
1.3861-1.40780.22461740.168217952X-RAY DIFFRACTION97
1.4078-1.43090.20022000.161917883X-RAY DIFFRACTION97
1.4309-1.45560.17921800.160417971X-RAY DIFFRACTION97
1.4556-1.4820.21022010.154317988X-RAY DIFFRACTION98
1.482-1.51050.16432030.134117953X-RAY DIFFRACTION98
1.5105-1.54140.14871950.121418013X-RAY DIFFRACTION98
1.5414-1.57490.13041510.115318085X-RAY DIFFRACTION98
1.5749-1.61150.1471720.111718165X-RAY DIFFRACTION98
1.6115-1.65180.12961720.109518097X-RAY DIFFRACTION98
1.6518-1.69650.12091920.114118196X-RAY DIFFRACTION99
1.6965-1.74640.16411910.116418162X-RAY DIFFRACTION99
1.7464-1.80280.13331700.118718228X-RAY DIFFRACTION99
1.8028-1.86720.14171900.122618249X-RAY DIFFRACTION99
1.8672-1.94190.15691930.122318307X-RAY DIFFRACTION99
1.9419-2.03030.13261510.121618383X-RAY DIFFRACTION99
2.0303-2.13740.13991850.121418336X-RAY DIFFRACTION99
2.1374-2.27120.14022200.125718381X-RAY DIFFRACTION100
2.2712-2.44660.1481720.133818453X-RAY DIFFRACTION100
2.4466-2.69270.15312210.139518468X-RAY DIFFRACTION100
2.6927-3.08220.14142030.141318518X-RAY DIFFRACTION100
3.0822-3.88250.15282150.132818601X-RAY DIFFRACTION100
3.8825-36.15270.15661820.138418557X-RAY DIFFRACTION99

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