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- PDB-4ptv: Halothermothrix orenii beta-glucosidase A, thiocellobiose complex -

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Basic information

Entry
Database: PDB / ID: 4ptv
TitleHalothermothrix orenii beta-glucosidase A, thiocellobiose complex
ComponentsGlycoside hydrolase family 1
KeywordsHYDROLASE / (beta/alpha)8 fold / TIM barrel / glycoside hydrolase / beta-glucosidase
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
thio-beta-cellobiose / : / Beta-glucosidase
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHassan, N. / Nguyen, T.H. / Kori, L.D. / Patel, B.K.C. / Haltrich, D. / Divne, C. / Tan, T.C.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Biochemical and structural characterization of a thermostable beta-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis.
Authors: Hassan, N. / Nguyen, T.H. / Intanon, M. / Kori, L.D. / Patel, B.K. / Haltrich, D. / Divne, C. / Tan, T.C.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 1
B: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2628
Polymers104,5712
Non-polymers1,6916
Water7,512417
1
A: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1314
Polymers52,2861
Non-polymers8463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1314
Polymers52,2861
Non-polymers8463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.753, 99.068, 108.090
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 Glycoside hydrolase family 1


Mass: 52285.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: bgla, Hore_15280 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8CYA8, beta-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose / thio-beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: thio-beta-cellobiose
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 45.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, CsCl2, PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2012 / Details: mirrors, Pt-coated
RadiationMonochromator: horizontally side diffracting Si(111) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.85→49.534 Å / Num. all: 80889 / Num. obs: 80889 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rsym value: 0.253 / Net I/σ(I): 12.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 6154 / Rsym value: 1.866 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TA9

3ta9


Resolution: 1.85→49.53 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2006 2.49 %random
Rwork0.1958 ---
all0.1966 80626 --
obs0.1966 80626 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 96 417 7809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087659
X-RAY DIFFRACTIONf_angle_d1.09510375
X-RAY DIFFRACTIONf_dihedral_angle_d14.5642906
X-RAY DIFFRACTIONf_chiral_restr0.0771036
X-RAY DIFFRACTIONf_plane_restr0.0051338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89630.39021480.33745573100
1.8963-1.94760.58881260.4703532095
1.9476-2.00490.26441330.27015556100
2.0049-2.06960.28341540.24515570100
2.0696-2.14350.29881530.25065571100
2.1435-2.22940.25021340.20295552100
2.2294-2.33080.30351330.23855612100
2.3308-2.45370.22181530.18095608100
2.4537-2.60740.23581480.18255605100
2.6074-2.80870.19231360.17695637100
2.8087-3.09140.20871500.17315664100
3.0914-3.53860.1881420.16195667100
3.5386-4.45780.14051470.1415724100
4.4578-49.55170.18191490.15915961100
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)
10.62050.1037-0.03651.08460.22370.97540.00390.00660.05870.10180.00560.03190.0221-0.04610.01190.03320.00220.0040.04710.02550.05362.0459106.452724.9252
20.9785-0.104-0.02910.7882-0.07591.29620.05760.0229-0.052-0.1058-0.02420.06580.1153-0.0161-0.01290.0754-0.0032-0.01980.02650.00210.06444.169499.925711.2549
30.9505-0.2522-0.09440.89210.41140.83370.05840.17770.0261-0.392-0.0129-0.0211-0.18820.0096-0.01860.1641-0.00470.00590.12290.02910.04695.5015109.9155-1.4058
40.9008-0.3986-0.58350.64770.33961.67960.00880.1140.2259-0.2572-0.0931-0.5875-0.30820.0828-0.32160.2144-0.03330.12420.14940.07510.236614.3982125.79594.0827
50.6084-0.0068-0.37110.99910.17030.83910.01590.02090.1095-0.0795-0.00360.1145-0.2837-0.1287-0.00510.11370.051500.04260.0260.1085-1.9778123.396217.7568
61.00810.1073-0.11590.8396-0.00521.03060.05420.0314-0.0017-0.03310.0113-0.0657-0.09270.097-0.01090.0480.00230.00890.0599-0.01570.053440.368490.70352.6866
70.9264-0.0343-0.0790.5995-0.19181.20620.0002-0.0375-0.1467-0.0020.02950.05980.1093-0.0437-0.01970.0510.0002-0.00560.04770.01420.08535.080183.22316.616
81.1313-0.1433-0.13930.9393-0.14531.0135-0.0579-0.48630.02880.33110.1550.0464-0.04220.2322-0.00350.13720.0024-0.0120.21940.00340.060540.190989.950127.26
91.150.791-0.82610.5872-0.54571.72210.3113-0.27070.6064-0.02260.13320.035-0.67140.1416-0.09910.2995-0.08860.02170.2513-0.08670.232549.7397105.49422.2627
100.92610.0951-0.18120.77150.41291.0522-0.0134-0.0761-0.04150.05260.04-0.2323-0.16570.36630.03530.0324-0.0189-0.020.1795-0.00740.114355.39590.00278.0535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4:136 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 137:211 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 212:303 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 304:330 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 331:448 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 4:48 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 49:211 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 212:303 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 304:330 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 331:448 )

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