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- PDB-1w3j: Family 1 b-glucosidase from Thermotoga maritima in complex with t... -

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Basic information

Entry
Database: PDB / ID: 1w3j
TitleFamily 1 b-glucosidase from Thermotoga maritima in complex with tetrahydrooxazine
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLUCOSIDE HYDROLYSIS / FAMILY GH1 / ENZYME / TETRAHYDROOXAZINE
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
TETRAHYDROOXAZINE / Beta-glucosidase A
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / Davies, G.J.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural, Thermodynamic, and Kinetic Analyses of Tetrahydrooxazine-Derived Inhibitors Bound to {Beta}-Glucosidases
Authors: Gloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / 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
DepositionJul 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2004Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS 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
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1804
Polymers107,8812
Non-polymers2982
Water9,926551
1
A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0902
Polymers53,9411
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0902
Polymers53,9411
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.562, 94.595, 113.480
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 446
2113B1 - 446

NCS oper: (Code: given
Matrix: (-0.01077, -0.98886, -0.14847), (0.98899, 0.01138, -0.14753), (0.14757, -0.14843, 0.97785)
Vector: -31.23118, 29.29491, 12.72239)

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Components

#1: Protein BETA-GLUCOSIDASE / / 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-OXZ / TETRAHYDROOXAZINE


Mass: 149.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSOME RESIDUES MISSING DUE TO POOR OR ABSENT DENSITY. THE FULL LENGTH PROTEIN ALSO CONTAINS A HIS- ...SOME RESIDUES MISSING DUE TO POOR OR ABSENT 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 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 7
Details: 10MG/ML PROTEIN IN 15% PEG 4000, 0.2 M CAAC, 0.1 M IMIDAZOLE PH7, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2003 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 66518 / % possible obs: 95.7 % / Redundancy: 5.22 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.12 / % possible all: 100

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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: 2→72.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.122 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3277 4.9 %RANDOM
Rwork0.204 ---
obs0.207 63027 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 20 551 7767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.92810193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12823.782394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.535151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8771544
X-RAY DIFFRACTIONr_chiral_restr0.1070.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.54516
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34527093
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98933532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9264.53100
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
1756tight positional0.070.05
1761loose positional0.455
1756tight thermal0.350.5
1761loose thermal2.210
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 258
Rwork0.262 4833

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