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- PDB-2vrj: Beta-glucosidase from Thermotoga maritima in complex with N-octyl... -

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Basic information

Entry
Database: PDB / ID: 2vrj
TitleBeta-glucosidase from Thermotoga maritima in complex with N-octyl-5- deoxy-6-oxa-N-(thio)carbamoylcalystegine
ComponentsBETA-GLUCOSIDASE A
KeywordsHYDROLASE / CALYSTEGINE / GLYCOSIDE HYDROLASE / FAMILY 1 / INHIBITOR / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION / CELLULOSE DEGRADATION / CARBOHYDRATE METABOLISM
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
ACETATE ION / Chem-NCW / Beta-glucosidase A
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAguilar, M. / Gloster, T.M. / Garcia-Moreno, M.I. / Ortiz Mellet, C. / Davies, G.J. / Llebaria, A. / Casas, J. / Egido-Gabas, M. / Garcia Fernandez, J.M.
CitationJournal: Chembiochem / Year: 2008
Title: Molecular Basis for Beta-Glucosidase Inhibition by Ring-Modified Calystegine Analogues.
Authors: Aguilar, M. / Gloster, T.M. / Garcia-Moreno, M.I. / Ortiz Mellet, C. / Davies, G.J. / Llebaria, A. / Casas, J. / Egido-Gabas, M. / Garcia Fernandez, J.M.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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)108,8049
Polymers107,8812
Non-polymers9227
Water12,052669
1
A: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4315
Polymers53,9411
Non-polymers4914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3724
Polymers53,9411
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.696, 94.409, 113.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 53940.648 Da / Num. of mol.: 2 / Fragment: 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: Chemical ChemComp-NCW / (1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide


Mass: 332.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28N2O4S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 7
Details: 10 MG/ML PROTEIN. 0.1 M IMIDAZOLE, PH 7, 0.2 M CALCIUM ACETATE, 14-19% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9753
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 79606 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD0

1od0


Resolution: 1.9→72.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.193 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3981 5 %RANDOM
Rwork0.195 ---
obs0.197 75551 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7125 0 58 669 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.93610446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93623.632402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.591151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7841550
X-RAY DIFFRACTIONr_chiral_restr0.10.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216092
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_it0.7461.54480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26127230
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92233174
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9274.53186
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 281
Rwork0.24 5462
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
11.23115.071312.0545
2-14.2339-32.6443-3.2693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 445
2X-RAY DIFFRACTION2B3 - 445

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