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- PDB-1od0: Family 1 b-glucosidase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1od0
TitleFamily 1 b-glucosidase from Thermotoga maritima
ComponentsBETA-GLUCOSIDASE A
KeywordsHYDROLASE / GLUCOSIDE HYDROLYSIS / FAMILY GH1 / ENZYME / GLYCOSIDASE / CELLULOSE DEGRADATION
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process
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
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsGloster, T. / Zechel, D.L. / Boraston, A.B. / Boraston, C.M. / Macdonald, J.M. / Tilbrook, D.M. / Stick, R.V. / Davies, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Iminosugar Glycosidase Inhibitors: Structural and Thermodynamic Dissection of the Binding of Isofagomine and 1-Deoxynojirimycin to Beta-Glucosidases
Authors: Zechel, D.L. / Boraston, A.B. / Gloster, T. / Boraston, C.M. / Macdonald, J.M. / Tilbrook, D.M. / Stick, R.V. / Davies, G.J.
History
DepositionFeb 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: 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-GLUCOSIDASE A
B: BETA-GLUCOSIDASE A


Theoretical massNumber of molelcules
Total (without water)107,8812
Polymers107,8812
Non-polymers00
Water9,746541
1
A: BETA-GLUCOSIDASE A


Theoretical massNumber of molelcules
Total (without water)53,9411
Polymers53,9411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE A


Theoretical massNumber of molelcules
Total (without water)53,9411
Polymers53,9411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.313, 94.547, 113.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSAA3 - 30125 - 323
21VALVALLYSLYSBB3 - 30125 - 323
12PHEPHELEULEUAA312 - 444334 - 466
22PHEPHELEULEUBB312 - 444334 - 466

NCS oper: (Code: given
Matrix: (0.99952, -0.02596, 0.01718), (0.02609, 0.99963, -0.00783), (-0.01697, 0.00827, 0.99982)
Vector: -0.62059, -0.60239, 0.40546)

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Components

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


Mass: 53940.648 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 2-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q08638, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA1,2,305-307,446, B307,B213,B446 POOR OR MISSING DENSITY THE FULL LENGTH PROTEIN ALSO CONTAINS A ...A1,2,305-307,446, B307,B213,B446 POOR OR MISSING DENSITY THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS-TAG FROM THE PET28A CLONING VECTOR. NUMBERING OF THE PROTEIN AGREES WITH THE SWISSPROT ENTRY AND THUS 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 7
Details: 10MG/ML PROTEIN IN 15% PEG 4K, 0.2 M CA ACETATE, 0.1M IMIDAZOLE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 58694 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.6
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.44 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.03refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOX

1qox


Resolution: 2.11→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.521 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A1,2,305-307,446, B307,B213,B446 POOR OR MISSING DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2960 5 %RANDOM
Rwork0.21 ---
obs0.213 55673 99.1 %-
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: 35.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 0 541 7676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217367
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.91710020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875875
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_restr0.0850.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.23144
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_refined0.3150.262
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
1700tight positional0.060.05
1709loose positional0.385
1700tight thermal0.280.5
1709loose thermal2.210
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 211
Rwork0.266 3881

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