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- PDB-4ptx: Halothermothrix orenii beta-glucosidase A, glucose complex -

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Basic information

Entry
Database: PDB / ID: 4ptx
TitleHalothermothrix orenii beta-glucosidase A, glucose complex
ComponentsGlycoside hydrolase family 1
KeywordsHYDROLASE / (beta/alpha)8 fold / TIM barrel / glycoside hydrolase / beta-glucosidase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / 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
beta-D-glucopyranose / CACODYLATE ION / Beta-glucosidase
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 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 1.3Nov 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)105,2056
Polymers104,5712
Non-polymers6344
Water7,404411
1
A: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6033
Polymers52,2861
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6033
Polymers52,2861
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.446, 97.878, 109.875
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: sodium cacodylate, MgCl2, PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: channel cut ESRF monochromator, Si(111) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93935 Å / Relative weight: 1
ReflectionResolution: 1.8→46.813 Å / Num. all: 88436 / Num. obs: 88436 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.181 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 12942 / Rsym value: 0.2228 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TA9

3ta9


Resolution: 1.8→46.81 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2000 2.26 %RANDOM
Rwork0.1827 ---
all0.1837 88435 --
obs0.1837 88435 98.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 34 411 7741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077565
X-RAY DIFFRACTIONf_angle_d1.07510261
X-RAY DIFFRACTIONf_dihedral_angle_d13.2732789
X-RAY DIFFRACTIONf_chiral_restr0.0461033
X-RAY DIFFRACTIONf_plane_restr0.0051332
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 (%)
1.8-1.8450.37281390.3286601697
1.845-1.89490.35061400.281604897
1.8949-1.95070.28811400.2467604498
1.9507-2.01360.25771400.2155607898
2.0136-2.08560.25311420.2101610998
2.0856-2.16910.22491410.1972610398
2.1691-2.26780.251420.1906612298
2.2678-2.38740.25291420.1907614798
2.3874-2.53690.28021430.1872617399
2.5369-2.73280.25121430.1913620899
2.7328-3.00780.23121440.1978620999
3.0078-3.44290.21731460.1849628299
3.4429-4.33720.1761450.1453632699
4.3372-46.82860.16931530.1396657099
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)
10.3631-0.14270.31750.7018-0.30180.52750.0313-0.0113-0.0123-0.0593-0.0125-0.00440.07990.00370.09780.07650.0225-0.00180.08320.0020.10443.3005103.649519.7445
20.49720.089-0.03860.5353-0.11590.29640.12410.31410.0858-0.6203-0.0550.11620.23810.10090.06380.29750.07810.04070.18330.01190.0445.1606106.9134-2.9274
30.0412-0.006-0.00080.00840.03480.0684-0.02110.1478-0.1358-0.38450.0133-0.1944-0.02950.1258-0.00060.2543-0.010.11510.23370.01360.207712.1905118.3807-0.7616
40.1381-0.1599-0.05970.16940.06990.04760.02660.08220.0904-0.338-0.0502-0.0205-0.13310.04680.00070.2364-0.0098-0.00450.16370.03390.13851.8426121.82064.4514
50.1003-0.0251-0.09840.2644-0.07050.1577-0.0580.03460.0216-0.02540.0543-0.0578-0.225-0.04640.00080.19320.0168-0.03780.07830.0120.1437-0.0429125.515617.5847
60.06920.0488-0.10080.1653-0.04320.1438-0.0768-0.05860.1390.25250.0079-0.0998-0.1555-0.04760.00020.18930.0249-0.03630.1187-0.00780.16232.4143123.726.3467
70.15360.1062-0.18720.08-0.06890.3247-0.0050.08080.0644-0.03450.0356-0.0596-0.0787-0.03320.00420.09780.032-0.00450.1299-0.01590.130141.718987.0917-1.898
80.1959-0.0292-0.0910.2334-0.20780.4854-0.0276-0.0075-0.03120.05440.05680.00630.0368-0.044200.11280.02420.0150.1243-0.01780.142533.466580.98985.6168
90.2757-0.10330.01170.1366-0.10.3403-0.1503-0.3172-0.10170.27730.19120.0670.0266-0.01690.01770.22780.09010.01220.2192-0.00370.1235.913284.86224.9886
100.05910.0422-0.07320.0211-0.03350.0536-0.0588-0.24140.11650.38350.17470.0144-0.02930.19690.00470.29740.046-0.00240.2429-0.1210.188745.497197.599324.75
110.1049-0.2004-0.05650.38470.08660.196-0.0889-0.24340.12230.0820.2498-0.3287-0.09840.19070.06460.18920.0595-0.08420.2121-0.0430.090852.911989.386519.6927
120.0419-0.0651-0.01790.17770.08790.1037-0.0292-0.02990.00330.08710.1786-0.1215-0.14630.37090.11050.05960.0192-0.05690.2557-0.07150.20257.045188.75756.5018
130.06230.0528-0.02650.11120.02670.1996-0.00740.13530.0622-0.03610.0849-0.1498-0.12530.19660.03790.07470.0205-0.01040.2249-0.03990.178454.4289.7263-2.1712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4:211 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 212:289 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 290:315 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 316:354 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 355:408 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 409:448 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 4:71 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 72:186 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 187:289 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 290:315 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 316:354 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 355:408 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 409:448 )

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