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

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Basic information

Entry
Database: PDB / ID: 1uwr
TitleStructure of beta-glycosidase from Sulfolobus solfataricus in complex with 2-deoxy-2-fluoro-galactose
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 1 / 2-DEOXY-2-FLUORO-GALACTOSE HYDROLASE / ARCHAEON
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 / 2-deoxy-2-fluoro-alpha-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 1.2Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.type / _entity_src_gen.pdbx_host_org_cell_line ..._diffrn_detector.type / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain
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 / 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 / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)113,9425
Polymers113,5192
Non-polymers4233
Water11,277626
1
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)227,88410
Polymers227,0384
Non-polymers8476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+4/31
Buried area11020 Å2
ΔGint-61 kcal/mol
Surface area78270 Å2
MethodPQS
Unit cell
Length a, b, c (Å)168.059, 168.059, 95.773
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: (-0.94239, 0.03327, -0.33287), (0.03208, -0.98147, -0.18893), (-0.33299, -0.18873, 0.92385)
Vector: 272.07199, 137.77603, 60.51359)

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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(DE3) / References: UniProt: P22498, beta-galactosidase
#2: Sugar ChemComp-GAF / 2-deoxy-2-fluoro-alpha-D-galactopyranose / 2-DEOXY-2-FLUORO-GALACTOSE / 2-deoxy-2-fluoro-alpha-D-galactose / 2-deoxy-2-fluoro-D-galactose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
a-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#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.: 626 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 85809 / % possible obs: 99.9 % / Redundancy: 5.89 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.86 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.82 / % possible all: 100

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Processing

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

1uwq


Resolution: 2.14→141.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.82 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: RESIDUES OMITTED DUE TO POOR OR MISSING DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4268 5 %RANDOM
Rwork0.19 ---
obs0.192 81104 98.9 %-
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: 41.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0.77 Å20 Å2
2---1.53 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.14→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7881 0 26 626 8533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0218191
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.92511147
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945969
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_restr0.0980.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026523
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23670
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.2107
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7181.54833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37927763
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12633358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3034.53384
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
1936tight positional0.050.05
1953loose positional0.35
1936tight thermal0.240.5
1953loose thermal1.9910
LS refinement shellResolution: 2.14→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 321
Rwork0.279 5663

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