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- PDB-2cbv: Beta-glucosidase from Thermotoga maritima in complex with calyste... -

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Basic information

Entry
Database: PDB / ID: 2cbv
TitleBeta-glucosidase from Thermotoga maritima in complex with calystegine B2
ComponentsBETA-GLUCOSIDASE A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / INHIBITOR / TRANSITION STATE MIMIC / FAMILY 1 / CARBOHYDRATE METABOLISM / CELLULOSE DEGRADATION / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / 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
ACETATE ION / CALYSTEGINE B2 / Beta-glucosidase A
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGloster, T.M. / Madsen, R. / Davies, G.J.
Citation
Journal: Chembiochem / Year: 2006
Title: Dissection of Conformationally Restricted Inhibitors Binding to a Beta-Glucosidase.
Authors: Gloster, T.M. / Madsen, R. / Davies, G.J.
#1: Journal: J.Am.Chem.Soc. / Year: 2007
Title: Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics.
Authors: Gloster, T.M. / Meloncelli, P. / Stick, R.V. / Zechel, D. / Vasella, A. / Davies, G.J.
History
DepositionJan 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3506
Polymers107,8812
Non-polymers4684
Water12,412689
1
A: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1753
Polymers53,9411
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1753
Polymers53,9411
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.261, 94.310, 113.411
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 444 / Label seq-ID: 25 - 466

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

NCS oper: (Code: given
Matrix: (-0.02441, -0.99027, -0.13702), (0.98993, -0.00482, -0.14149), (0.13945, -0.1391, 0.98041)
Vector: -31.52461, 28.50126, 13.01872)

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Components

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


Mass: 53940.648 Da / Num. of mol.: 2
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: Chemical ChemComp-CGB / CALYSTEGINE B2 / (1S,2R,3S,4R,5S)-8-AZABICYCLO[3.2.1]OCTANE-1,2,3,4-TETROL


Mass: 175.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYSES THE TERMINAL, NON-REDUCING BETA-D- GLUCOSE RESIDUES WITH RELEASE OF BETA-D-GLUCOSE
Sequence detailsSEQUENCE CONTAINS THE HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING IN THE CO-ORDINATES REFERS TO ...SEQUENCE CONTAINS THE HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING IN THE CO-ORDINATES REFERS TO THE UNIPROT AND IGNORE 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: 47 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 7
Details: 10 MG/ML PROTEIN, 15% PEG 4K, 0.1 M IMIDAZOLE, PH 7, 0.2 M CALCIUM ACETATE, 25% ETHYLENE GLYCOL AS CRYO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9747
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 73572 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.37
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.81 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD0

1od0


Resolution: 1.95→72.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.826 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3701 5 %RANDOM
Rwork0.183 ---
obs0.186 69755 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7207 0 32 689 7928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.93510576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79723.725408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.178151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1011550
X-RAY DIFFRACTIONr_chiral_restr0.0990.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23827
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25193
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2584
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.54669
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23127315
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88233653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7584.53223
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
1746medium positional0.160.5
1766loose positional0.385
1746medium thermal3.322
1766loose thermal4.1210
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 263
Rwork0.236 5017

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