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- PDB-1uwt: Structure of beta-glycosidase from Sulfolobus solfataricus in com... -

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Basic information

Entry
Database: PDB / ID: 1uwt
TitleStructure of beta-glycosidase from Sulfolobus solfataricus in complex with D-galactohydroximo-1,5-lactam
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 1 / ARCHAEON D-GALACTOHYDROXIMO-1 / 5-LACTAM
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / beta-glucosidase 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 ...: / 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 / Chem-GTL / Beta-galactosidase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGloster, T.M. / Roberts, S. / Ducros, V.M.-A. / Perugino, G. / Rossi, M. / Hoos, R. / Moracci, M. / Vasella, A. / Davies, G.J.
CitationJournal: Biochemistry / Year: 2004
Title: Structural studies of the beta-glycosidase from Sulfolobus solfataricus in complex with covalently and noncovalently bound inhibitors.
Authors: Gloster, T.M. / Roberts, S. / Ducros, V.M. / Perugino, G. / Rossi, M. / Hoos, R. / Moracci, M. / Vasella, A. / Davies, G.J.
History
DepositionFeb 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Dec 13, 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 / struct_ncs_dom_lim / 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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 9-STRANDED BARRELS REPRESENTED BY 10-STRANDED SHEETS 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)113,9625
Polymers113,5192
Non-polymers4433
Water16,484915
1
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)227,92410
Polymers227,0384
Non-polymers8876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+4/31
MethodPQS
Unit cell
Length a, b, c (Å)168.300, 168.300, 95.670
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: 3 / Auth seq-ID: 1 - 489 / Label seq-ID: 1 - 489

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

NCS oper: (Code: given
Matrix: (-0.94126, 0.03409, -0.33596), (0.03189, -0.98147, -0.18894), (-0.33617, -0.18856, 0.92273)
Vector: 271.70193, 137.67532, 60.93724)

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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 BL21 (bacteria) / References: UniProt: P22498, beta-galactosidase
#2: Chemical ChemComp-GTL / (2E,3R,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)-2-PIPERIDINONE / D-GALACTOHYDROXIMO-1,5-LACTAM


Mass: 192.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 63.5 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 4.6
Details: 11-14% PEG 4K, 0.1 M NA ACETATE, 0.2 M AMMONIUM ACETATE. CRYO - 25% ETHYLENE GLYCOL, 10-13 MG/ML PROTEIN, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111), SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 113580 / % possible obs: 100 % / Redundancy: 7.13 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.06 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4.48 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWQ

1uwq


Resolution: 1.95→141.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.854 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: RESIDUES OMITTED DUE TO POOR OR MISSING DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5527 5 %RANDOM
Rwork0.201 ---
obs0.203 104713 96.9 %-
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: 36.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å2-1.05 Å20 Å2
2---2.11 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.95→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 30 915 8830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.92411219
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23897
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2652
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.54826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38427778
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.24233419
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3394.53441
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
1935tight positional0.050.05
1963loose positional0.395
1935tight thermal0.290.5
1963loose thermal1.9910
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 400
Rwork0.307 7597

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