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- PDB-4gxp: Chimeric Family 1 beta-glucosidase made with non-contiguous SCHEMA -

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Basic information

Entry
Database: PDB / ID: 4gxp
TitleChimeric Family 1 beta-glucosidase made with non-contiguous SCHEMA
ComponentsBeta-glucosidase Chimeric protein
KeywordsHYDROLASE / chimeragenesis / protein recombination / eukaryotic-prokaryotic chimera / GH1 / beta-glucosidase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / carbohydrate metabolic 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
Beta-glucosidase / Beta-glucosidase A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Trichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSmith, M.A. / Romero, P.A. / Wu, T. / Brustad, E.M. / Arnold, F.H.
CitationJournal: Protein Sci. / Year: 2013
Title: Chimeragenesis of distantly-related proteins by noncontiguous recombination.
Authors: Smith, M.A. / Romero, P.A. / Wu, T. / Brustad, E.M. / Arnold, F.H.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase Chimeric protein
B: Beta-glucosidase Chimeric protein
C: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)159,0793
Polymers159,0793
Non-polymers00
Water362
1
A: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucosidase Chimeric protein


Theoretical massNumber of molelcules
Total (without water)53,0261
Polymers53,0261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.377, 115.377, 282.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Beta-glucosidase Chimeric protein / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 53026.301 Da / Num. of mol.: 3
Fragment: UNP Q08638 residues 1-160,204-217,352-380,395-446 and UNP O93785 residues 160-302,221-367,399-413
Mutation: Y120F,W134L,A135L,H378Y,Q336A,S337M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria), (gene. exp.) Trichoderma reesei (fungus)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: bglA, bgl2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08638, UniProt: O93785, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% polyethylene glycol 3350, 0.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012
RadiationMonochromator: Liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→37.43 Å / Num. all: 43376 / Num. obs: 43376 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.052 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3-3.164.80.38120.381199.6
3.16-3.355.30.2423.10.242199.8
3.35-3.5950.1435.10.143199.8
3.59-3.875.10.097.80.09199.8
3.87-4.2450.0689.30.068199.8
4.24-4.744.70.05111.80.051199.8
4.74-5.484.90.04414.20.044199.5
5.48-6.714.80.03716.70.037199.7
6.71-9.494.70.0319.20.03199.3
9.49-37.4294.60.02523.10.025197.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XSCALEdata scaling
MOLREP(CCP4 6.2)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 59.565 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R: 1.788 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29377 2188 5.1 %RANDOM
Rwork0.2389 ---
obs0.24164 41124 99.47 %-
all-43315 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 3→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9867 0 0 2 9869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.90813956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70851360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35223.124461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.927151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0291555
X-RAY DIFFRACTIONr_chiral_restr0.1240.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218412
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 165 -
Rwork0.324 2841 -
obs--99.21 %
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)
10.1616-0.14340.40360.65950.06842.247-0.1284-0.2135-0.2314-0.29650.29220.0707-0.5830.0078-0.16381.0373-0.19240.01571.67350.06671.22912.408213.14721.653
21.52170.50580.41150.2503-0.05441.11510.0939-0.0877-0.3299-0.030.03790.0836-0.020.3401-0.13170.53530.1706-0.10122.1206-0.05151.292923.4516-16.507337.1928
31.770.1145-0.45930.4556-0.56871.52250.18581.2683-0.08640.2211-0.49170.2006-0.21360.89980.30590.2353-0.0802-0.053.4640.3040.866362.05360.177916.4891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 466
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B11 - 466
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C11 - 467

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