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- PDB-4ptw: Halothermothrix orenii beta-glucosidase A, 2-deoxy-2-fluoro-gluco... -

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Basic information

Entry
Database: PDB / ID: 4ptw
TitleHalothermothrix orenii beta-glucosidase A, 2-deoxy-2-fluoro-glucose 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
2-deoxy-2-fluoro-alpha-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 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 1.4Nov 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)105,3246
Polymers104,5712
Non-polymers7534
Water7,368409
1
A: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6623
Polymers52,2861
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6623
Polymers52,2861
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.983, 97.540, 109.616
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-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, sodium acetate, 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: 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: 2→47.781 Å / Num. all: 64629 / Num. obs: 64629 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.157 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 8644 / Rsym value: 1.31 / % possible all: 98.8

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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: 2→47.78 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2000 3.09 %random
Rwork0.1774 ---
all0.1792 64627 --
obs0.1792 64627 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 46 409 7751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087566
X-RAY DIFFRACTIONf_angle_d1.06510247
X-RAY DIFFRACTIONf_dihedral_angle_d16.3552793
X-RAY DIFFRACTIONf_chiral_restr0.0751030
X-RAY DIFFRACTIONf_plane_restr0.0041329
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 (%)
2-2.050.31091390.264436699
2.05-2.10550.3451420.2467440799
2.1055-2.16740.32421400.2304443799
2.1674-2.23740.28151410.2168438999
2.2374-2.31730.31511420.2191443899
2.3173-2.41010.28331410.1932441999
2.4101-2.51980.20261410.1833442699
2.5198-2.65260.26431420.1793444899
2.6526-2.81880.26051430.1831448499
2.8188-3.03640.24891440.18754483100
3.0364-3.34190.22281430.1734492100
3.3419-3.82530.20291440.15364534100
3.8253-4.81880.16231470.13224567100
4.8188-47.79510.22221510.1675473799
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)
10.01630.00880.00460.02110.0050.00960.01070.00950.01550.00580.0056-0.00640.00350.00380.01470.02260.0279-0.02190.02810.00810.0846.8132109.86722.705
20.00610.00170.00780.00170.00030.04370.0213-0.040.04290.0401-0.01130.01040.0307-0.06220.00260.05780.01240.00690.0546-0.01020.0758-0.8948105.392628.9019
30.0101-0.0120.02580.0299-0.03350.06510.05280.0209-0.0222-0.1065-0.01020.0050.05270.0120.02080.06410.02590.00150.0433-0.00410.07164.22599.481312.7353
40.0282-0.01270.01140.06180.04030.04510.030.09010.0061-0.152-0.0103-0.01370.0120.03790.0320.13910.04950.02830.0167-0.0518-0.07925.1875106.7447-2.9272
50.0073-0.007-0.01080.00560.00690.0177-0.00670.02570.0023-0.07180.0218-0.0669-0.04170.0250.00970.09160.00340.06610.05730.01390.078412.2075118.2684-0.837
60.0132-0.0078-0.01030.0135-0.01040.03650.04810.01150.0106-0.0626-0.0120.0075-0.03380.00530.06120.14890.0017-0.04820.03110.02480.0431.8941121.60544.3288
70.017-0.00780.00370.0241-0.00450.00120.01290.0210.0293-0.00580.0013-0.0274-0.0775-0.0140.03160.17870.0543-0.0775-0.04260.01710.0987-0.1597125.292717.6026
80.00830.0122-0.00270.0198-0.00220.0020.0029-0.02340.0280.0415-0.0034-0.0025-0.0452-0.0055-0.00050.11370.0508-0.06510.00590.00630.07872.1586123.373226.3278
90.03340.00470.01440.0075-0.01760.0531-0.0071-0.00880.0109-0.01280.0236-0.0394-0.05060.02550.0150.04290.0547-0.00370.0887-0.02460.100341.643786.9014-1.7029
100.0118-0.0033-0.00790.0145-0.00320.0173-0.01020.0113-0.0225-0.00110.017-0.02920.012-0.00820.00660.04450.03470.03490.0847-0.03340.103135.512776.7226-1.8933
110.0222-0.006-0.00040.02130.00510.00570.015-0.0724-0.05320.0440.04690.0046-0.0114-0.05350.1227-0.10710.0990.10320.014-0.0518-0.003131.645882.001911.9181
120.1037-0.0279-0.08620.0453-0.01180.10550.0116-0.1667-0.00280.13030.1045-0.0006-0.01420.0670.09660.11870.09350.02080.1811-0.04-0.004339.778887.44426.3529
130.00660.0015-0.0020.00120.00110.00220.00170.00060.01020.01530.0023-0.0057-0.01840.0134-0.00130.1543-0.03380.01690.117-0.12260.112449.6482102.671121.4199
140.0017-0.0014-0.00090.0003-0.00020.00380.0082-0.0336-0.0140.01550.0294-0.0140.01590.00760.0260.11080.0856-0.06490.2223-0.00250.073851.380481.264222.6379
150.0597-0.02410.01030.03-0.00050.00210.0005-0.0485-0.02740.02110.0695-0.0584-0.00950.08140.0745-0.06470.0312-0.0420.1219-0.05660.079657.059788.38836.7004
160.0015-0.001-0.00370.00630.00760.01140.00340.0094-0.003-0.01460.043-0.0811-0.00370.07250.02650.0101-0.00650.01140.1358-0.03970.105354.240489.534-1.9949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4:48 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 49:110 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 111:211 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 212:289 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 290:315 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 316:354 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 355:408 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 409:448 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 4:71 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 72:110 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 111:211 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 212:303 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 304:330 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 331:354 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 355:408 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 409:448 )

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