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- PDB-2yfn: galactosidase domain of alpha-galactosidase-sucrose kinase, AgaSK -

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Basic information

Entry
Database: PDB / ID: 2yfn
Titlegalactosidase domain of alpha-galactosidase-sucrose kinase, AgaSK
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
PHOSPHATE ION / Bifunctional alpha-galactosidase/sucrose kinase AgaSK
Similarity search - Component
Biological speciesRUMINOCOCCUS GNAVUS E1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)81,7217
Polymers81,3311
Non-polymers3906
Water19,0601058
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)326,88428
Polymers325,3254
Non-polymers1,55924
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 area26650 Å2
ΔGint-114.9 kcal/mol
Surface area83260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.058, 111.650, 154.886
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-2058-

HOH

21A-2463-

HOH

31A-2521-

HOH

41A-3034-

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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Non-polymers , 5 types, 1064 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1058 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 57 % / 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: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→36 Å / Num. obs: 158241 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MI6

3mi6


Resolution: 1.45→36.19 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.828 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14957 8033 5.1 %RANDOM
Rwork0.13007 ---
obs0.13105 150207 98.75 %-
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: 13.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 23 1058 6795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226191
X-RAY DIFFRACTIONr_bond_other_d0.0010.024210
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9528458
X-RAY DIFFRACTIONr_angle_other_deg0.86310266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.725809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26324.118323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.319151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.031544
X-RAY DIFFRACTIONr_chiral_restr0.0910.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021323
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_it0.7521.53708
X-RAY DIFFRACTIONr_mcbond_other0.2351.51517
X-RAY DIFFRACTIONr_mcangle_it1.30326015
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0832483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3594.52395
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: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 525 -
Rwork0.24 10384 -
obs--92.83 %
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)
10.22310.00230.02290.0703-0.00850.07710.01380.00920.0211-0.02370.01210.0107-0.0252-0.0129-0.02590.03410.00390.00420.04280.01570.033138.31715.03351.433
20.3140.4185-0.15570.7342-0.55071.15820.0288-0.03320.03760.0686-0.0090.0684-0.1335-0.0043-0.01980.04260.01220.01320.04450.00820.038332.02320.26181.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 626
2X-RAY DIFFRACTION2A627 - 720

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