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- PDB-2ceq: Beta-glycosidase from Sulfolobus solfataricus in complex with glu... -

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Basic information

Entry
Database: PDB / ID: 2ceq
TitleBeta-glycosidase from Sulfolobus solfataricus in complex with glucoimidazole
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / ARCHAEON / FAMILY 1 / GLYCOSIDE HYDROLASE / GLUCOIMIDAZOLE / GLYCOSIDASE
Function / homology
Function and homology information


beta-galactosidase / beta-glucosidase activity / 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
ACETATE ION / GLUCOIMIDAZOLE / Beta-galactosidase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsGloster, T.M. / Moracci, M. / Vasella, A. / Davies, G.J.
CitationJournal: Biochemistry / Year: 2006
Title: Structural, Kinetic, and Thermodynamic Analysis of Glucoimidazole-Derived Glycosidase Inhibitors.
Authors: Gloster, T.M. / Roberts, S. / Perugino, G. / Rossi, M. / Moracci, M. / Panday, N. / Terinek, M. / Vasella, A. / Davies, G.J.
History
DepositionFeb 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2169
Polymers113,5192
Non-polymers6987
Water15,781876
1
A: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0794
Polymers56,7591
Non-polymers3193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1385
Polymers56,7591
Non-polymers3784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.927, 167.927, 93.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 5 / Auth seq-ID: 1 - 489 / Label seq-ID: 1 - 489

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.942, 0.034, -0.335), (0.032, -0.981, -0.189), (-0.335, -0.189, 0.923)
Vector: 271.26645, 137.54636, 60.68984)

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Components

#1: Protein BETA-GALACTOSIDASE / / BETA-GLYCOSIDASE / LACTASE


Mass: 56759.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P22498, beta-galactosidase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GIM / GLUCOIMIDAZOLE / (5S,6S,7R,8R)-5-(HYDROXYMETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL


Mass: 201.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYSIS OF TERMINAL NON-REDUCING BETA-D- GALACTOSE RESIDUES IN BETA-D-GALACTOSIDES

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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: 3.4 Å3/Da / Density % sol: 63 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 4.6
Details: 11-14 PEG 4K, 0.1 M SODIUM ACETATE, PH 4.6 0.2 AMMONIUM ACETATE, 10-13 MG/ML PROTEIN 25% ETHYLENE GLYCOL AS CRYO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2004 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 83599 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.94 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWQ

1uwq


Resolution: 2.14→145.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.243 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4163 5 %RANDOM
Rwork0.176 ---
obs0.178 79106 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.52 Å20 Å2
2---1.05 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.14→145.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 48 876 8916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.93711661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43951057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45223.101445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.286151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3781566
X-RAY DIFFRACTIONr_chiral_restr0.0970.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.24085
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2672
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.2124
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.55128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20628066
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78334058
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.584.53554
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1945medium positional0.190.5
1989loose positional0.395
1945medium thermal1.282
1989loose thermal1.9810
LS refinement shellResolution: 2.14→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 304
Rwork0.222 5667

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