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- PDB-4bce: crystal structure of Ttb-gly N282T mutant -

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Basic information

Entry
Database: PDB / ID: 4bce
Titlecrystal structure of Ttb-gly N282T mutant
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 1 / TRANSGLYCOSIDASE
Function / homology
Function and homology information


: / 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
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeze, D. / Tran, V. / Tellier, C. / Dion, M. / Leroux, C. / Roncza, J. / Czjzek, M.
CitationJournal: Protein Eng.Des.Sel. / Year: 2014
Title: Semi-Rational Approach for Converting a Gh1 Beta-Glycosidase Into a Beta-Transglycosidase.
Authors: Teze, D. / Hendrickx, J. / Czjzek, M. / Ropartz, D. / Sanejouand, Y. / Tran, V. / Tellier, C. / Dion, M.
History
DepositionOct 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Non-polymer description / Refinement description
Revision 1.2Dec 20, 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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" 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 "CA" 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
C: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)148,4603
Polymers148,4603
Non-polymers00
Water9,764542
1
A: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)49,4871
Polymers49,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)49,4871
Polymers49,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)49,4871
Polymers49,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.167, 77.665, 122.015
Angle α, β, γ (deg.)90.00, 100.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2100-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A6 - 429
2115B6 - 429
3115C6 - 429

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.254801, -0.005325, 0.966979), (0.006417, -0.999972, -0.003815), (0.966972, 0.005233, 0.254828)0.36353, 14.55784, -0.34422
3given(-0.628168, -0.609005, 0.484269), (-0.625408, 0.024926, -0.7799), (0.462892, -0.792774, -0.396535)-6.4664, 46.82632, 66.42419

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Components

#1: Protein BETA-GLUCOSIDASE / B-GLYCOSIDASE


Mass: 49486.766 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Plasmid: PBTAC2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): F' LACIQ
References: UniProt: Q53W75, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.4 % / Description: NONE
Crystal growpH: 6.5
Details: SODIUM CITRATE 0.4M, SODIUM CACODYLATE 0.1M, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.923
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 1.95→47.16 Å / Num. obs: 86355 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UG6

1ug6


Resolution: 2→39.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.107 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19015 4438 5 %RANDOM
Rwork0.15556 ---
obs0.15725 84077 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10199 0 0 542 10741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.01910617
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.95214495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58151284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63221.269536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.145151530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.12215135
X-RAY DIFFRACTIONr_chiral_restr0.1470.21469
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218567
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_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_restr8.536310615
X-RAY DIFFRACTIONr_sphericity_free4.7595188
X-RAY DIFFRACTIONr_sphericity_bonded3.707510637
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1676medium positional0.180.5
2B1676medium positional0.140.5
3C1676medium positional0.220.5
1A1674loose positional0.45
2B1674loose positional0.465
3C1674loose positional0.455
1A1676medium thermal3.232
2B1676medium thermal2.192
3C1676medium thermal3.972
1A1674loose thermal4.0910
2B1674loose thermal3.6710
3C1674loose thermal4.9610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 293 -
Rwork0.213 6017 -
obs--98.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2856-0.03970.03040.53750.25620.69490.036-0.04730.01910.0544-0.0425-0.00210.1352-0.05860.00650.0429-0.0314-0.01390.04650.00140.03533.344-8.36626.347
20.39370.1653-0.01730.840.21650.67150.01280.01630.015-0.01380.0162-0.0136-0.08780.0603-0.0290.0163-0.01510.01090.02320.00050.062924.89123.1769.715
30.69720.05920.13840.82210.12050.7560.0383-0.02310.09360.1054-0.0115-0.027-0.04360.0138-0.02680.0703-0.0483-0.00820.1135-0.03580.04529.95324.39663.704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 429
2X-RAY DIFFRACTION2B4 - 428
3X-RAY DIFFRACTION3C6 - 429

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