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- PDB-2yfo: GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK... -

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Basic information

Entry
Database: PDB / ID: 2yfo
TitleGALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, in complex with galactose
ComponentsALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
KeywordsHYDROLASE
Function / homology
Function and homology information


melibiose catabolic process / carbohydrate kinase activity / stachyose metabolic process / raffinose catabolic process / raffinose alpha-galactosidase activity / Transferases; Transferring phosphorus-containing groups / alpha-galactosidase / alpha-galactosidase activity / nucleotidyltransferase activity / protein homotetramerization ...melibiose catabolic process / carbohydrate kinase activity / stachyose metabolic process / raffinose catabolic process / raffinose alpha-galactosidase activity / Transferases; Transferring phosphorus-containing groups / alpha-galactosidase / alpha-galactosidase activity / nucleotidyltransferase activity / protein homotetramerization / magnesium ion binding / ATP binding
Similarity search - Function
alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / alpha-D-galactopyranose / TRIETHYLENE GLYCOL / PHOSPHATE ION / Bifunctional alpha-galactosidase/sucrose kinase AgaSK
Similarity search - Component
Biological speciesRUMINOCOCCUS GNAVUS E1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.35 Å
AuthorsSulzenbacher, G. / Bruel, L. / Tison-Cervera, M. / Pujol, A. / Nicoletti, C. / Perrier, J. / Galinier, A. / Ropartz, D. / Fons, M. / Pompeo, F. / Giardina, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Agask, a Bifunctional Enzyme from the Human Microbiome Coupling Galactosidase and Kinase Activities
Authors: Bruel, L. / Sulzenbacher, G. / Tison-Cervera, M. / Pujol, A. / Nicoletti, C. / Perrier, J. / Galinier, A. / Ropartz, D. / Fons, M. / Pompeo, F. / Giardina, T.
History
DepositionApr 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references / Derived calculations / Other
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,10036
Polymers81,3311
Non-polymers1,76935
Water19,2941071
1
A: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
hetero molecules

A: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
hetero molecules

A: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
hetero molecules

A: ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,400144
Polymers325,3254
Non-polymers7,075140
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_655-x+1,-y,z1
Buried area43490 Å2
ΔGint-1161.6 kcal/mol
Surface area80770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.016, 111.603, 155.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21A-2197-

HOH

31A-2468-

HOH

41A-3040-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALPHA-GALACTOSIDASE-SUCROSE KINASE AGASK


Mass: 81331.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINOCOCCUS GNAVUS E1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4T4R7*PLUS, alpha-galactosidase

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Sugars , 2 types, 2 molecules

#6: Sugar ChemComp-GLA / alpha-D-galactopyranose / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-GAL / beta-D-galactopyranose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1104 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1071 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGALACTOSE (GAL): GALACTOSE IS PRESENT AS MIXTURE OF ALPHA AND BETA CONFIGURATION
Sequence detailsSEQUENCE NOT AVAILABLE IN UNIPROT YET, BUT WILL BE DEPOSITED SOON. THE TREMBL ACCESSION ID IS FQ790379

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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: 2.84 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.5
Details: 14% PEG 8000, 0.1M HEPES PH 7.5, PROTEIN CONCENTRATION 7MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.35→47 Å / Num. obs: 198265 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 7.99 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.35→46.97 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.214 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14171 10028 5.1 %RANDOM
Rwork0.12436 ---
obs0.12524 188194 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.35→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 78 1071 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226274
X-RAY DIFFRACTIONr_bond_other_d0.0010.024275
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9568579
X-RAY DIFFRACTIONr_angle_other_deg1.093310446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87124.268328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.359151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.391543
X-RAY DIFFRACTIONr_chiral_restr0.0930.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021330
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.90823743
X-RAY DIFFRACTIONr_mcbond_other0.30121528
X-RAY DIFFRACTIONr_mcangle_it1.5212.56083
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.123.52531
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2574.52441
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 735 -
Rwork0.194 13810 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1386-0.00290.01570.05960.00340.05340.00940.01620.0149-0.01780.0050.0093-0.0165-0.0134-0.01430.01160.00380.00280.00810.00870.009638.096914.830251.0846
20.16810.1091-0.04480.2225-0.27280.67670.019-0.0270.02030.0396-0.0110.0243-0.09020.0129-0.0080.02330.00020.01020.00750.00170.010831.931720.109281.69
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 626
2X-RAY DIFFRACTION2A627 - 720

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