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- PDB-2wc3: Structure of family 1 beta-glucosidase from Thermotoga maritima i... -

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Basic information

Entry
Database: PDB / ID: 2wc3
TitleStructure of family 1 beta-glucosidase from Thermotoga maritima in complex with 3-imino-2-oxa-(+)-8-epi-castanospermine
ComponentsBETA-GLUCOSIDASE A
KeywordsHYDROLASE / CASTANOSPERMINE / GLYCOSIDE HYDROLASE / POLYSACCHARIDE DEGRADATION / CELLULOSE DEGRADATION / CARBOHYDRATE METABOLISM / FAMILY 1 / INHIBITORS / GLYCOSIDASE
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / 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, beta-glucosidase / 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
Chem-AM3 / Beta-glucosidase A
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAguilar, M. / Gloster, T.M. / Turkenburg, J.P. / Garcia-Moreno, M.I. / Ortiz Mellet, C. / Davies, G.J. / Garcia Fernandez, J.M.
CitationJournal: Org.Biomol.Chem. / Year: 2009
Title: Glycosidase Inhibition by Ring-Modified Castanospermine Analogues: Tackling Enzyme Selectivity by Inhibitor Tailoring.
Authors: Aguilar-Moncayo, M. / Gloster, T.M. / Turkenburg, J.P. / Garcia-Moreno, M.I. / Ortiz Mellet, C. / Davies, G.J. / Garcia Fernandez, J.M.
History
DepositionMar 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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_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_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" 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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" 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 "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A
C: BETA-GLUCOSIDASE A
D: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,0288
Polymers215,7634
Non-polymers1,2664
Water20,1411118
1
A: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2572
Polymers53,9411
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2572
Polymers53,9411
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2572
Polymers53,9411
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2572
Polymers53,9411
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.812, 73.965, 119.318
Angle α, β, γ (deg.)90.00, 108.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BETA-GLUCOSIDASE A / BETA-GLUCOSIDASE / GENTIOBIASE / CELLOBIASE / BETA-D-GLUCOSIDE GLUCOHYDROLASE


Mass: 53940.648 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q08638, beta-glucosidase
#2: Chemical
ChemComp-AM3 / (3Z,5S,6R,7S,8S,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol


Mass: 316.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CRYSTALLIZED CONTAINS AN N-TERMINAL HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING ...THE SEQUENCE CRYSTALLIZED CONTAINS AN N-TERMINAL HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING REFERS TO THE UNIPROT ENTRY AND IGNORES THE HIS TAG.

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7
Details: 10 MG/ML PROTEIN, 0.1 M IMIDAZOLE, PH7, 0.2 CALCIUM ACETATE, 15-17% PEG 4000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 112653 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD0

1od0


Resolution: 2→113.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.893 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5638 5 %RANDOM
Rwork0.184 ---
obs0.187 106573 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20.56 Å2
2---0.54 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14387 0 88 1118 15593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.93220631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08651827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64423.849782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06152352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.661584
X-RAY DIFFRACTIONr_chiral_restr0.10.22123
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111922
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6961.58879
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.196214346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.09536253
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1484.56255
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: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 427 -
Rwork0.245 7628 -
obs--94.75 %

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