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- PDB-3zjk: crystal structure of Ttb-gly F401S mutant -

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Basic information

Entry
Database: PDB / ID: 3zjk
Titlecrystal structure of Ttb-gly F401S mutant
ComponentsBETA GLYCOSIDASE
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJan 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 GLYCOSIDASE
B: BETA GLYCOSIDASE
C: BETA GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2159
Polymers145,8323
Non-polymers3836
Water7,224401
1
A: BETA GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7383
Polymers48,6111
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7383
Polymers48,6111
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7383
Polymers48,6111
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.557, 77.322, 101.767
Angle α, β, γ (deg.)90.00, 103.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96247, -0.00721, -0.27129), (-0.02077, -0.99476, 0.10015), (-0.27059, 0.10203, 0.95727)36.4129, -18.3783, 5.7611
2given(-0.99144, 0.08909, -0.09541), (0.0967, 0.01031, -0.99526), (-0.08769, -0.99597, -0.01883)-12.8087, 15.5563, 14.2853

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Components

#1: Protein BETA GLYCOSIDASE / BETA-GLYCOSIDASE


Mass: 48610.805 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Plasmid: PBTAC2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): F'LACIQ / References: UniProt: Q9RA61, beta-glucosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 5 RESIDUES AND LAST 3 RESIDUES ARE MISSING IN THE ELECTRON DENSITY AND THE PROTEIN ...THE FIRST 5 RESIDUES AND LAST 3 RESIDUES ARE MISSING IN THE ELECTRON DENSITY AND THE PROTEIN CONTAINS 2 POINT MUTATIONS Y320H AND F401S

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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: 2.73 Å3/Da / Density % sol: 54.9 % / 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: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.2→62 Å / Num. obs: 75663 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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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: 2.2→60.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.278 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT AND U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22289 3808 5 %RANDOM
Rwork0.17285 ---
obs0.17539 71835 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10179 0 21 401 10601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.95414361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58951269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42221.42528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.714151509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0715129
X-RAY DIFFRACTIONr_chiral_restr0.1230.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218460
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_restr10.756310527
X-RAY DIFFRACTIONr_sphericity_free4.4735188
X-RAY DIFFRACTIONr_sphericity_bonded3.945510413
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 267 -
Rwork0.238 5104 -
obs--99.19 %
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)
10.91060.25730.13351.00080.16930.80850.0056-0.06390.0166-0.0056-0.0272-0.0085-0.0551-0.04080.02160.03810.0233-0.01250.1084-0.0650.0983-0.6168.73639.609
21.1882-0.29710.29391.6650.51410.75640.09250.02-0.108-0.0143-0.07380.10440.0517-0.0574-0.01870.0354-0.00930.00010.0556-0.02430.139925.923-23.38845.372
31.46610.78510.47652.8120.97562.3589-0.15220.1721-0.3624-0.44720.1961-0.31130.0594-0.1765-0.04390.2363-0.07140.07510.1209-0.12620.1685-15.085-24.2655.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 904
2X-RAY DIFFRACTION2B6 - 903
3X-RAY DIFFRACTION3C5 - 429

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