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- PDB-9urf: Crystal structure of beta-glucosidase from Bacteroides ovatus -

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Basic information

Entry
Database: PDB / ID: 9urf
TitleCrystal structure of beta-glucosidase from Bacteroides ovatus
Componentsbeta-glucosidase
KeywordsHYDROLASE / Glycosidase / beta-glucosidase / beta-D-glucose
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / periplasmic space
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / : / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Periplasmic beta-glucosidase
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKumar, A.K. / Jamdar, S.N. / Sarver, R. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Atomic energy (DAE) India
CitationJournal: To Be Published
Title: Crystal structure of beta-glucosidase from Bacteroides ovatus
Authors: Kumar, A.K. / Jamdar, S.N. / Sarver, R. / Makde, R.D.
History
DepositionApr 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-glucosidase
B: beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,8064
Polymers179,7582
Non-polymers492
Water31,3281739
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-30 kcal/mol
Surface area49130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.653, 74.665, 86.751
Angle α, β, γ (deg.)72.859, 67.700, 64.776
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein beta-glucosidase


Mass: 89878.812 Da / Num. of mol.: 2 / Mutation: H625Q
Source method: isolated from a genetically manipulated source
Details: Streptavidin-His-Tev tag is not removed
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_03380 / Plasmid: pSTSTRHISN / Details (production host): Tan Lab pST44system / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0AAN3A6K2, beta-glucosidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1739 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 9.5 / Details: 0.1 M CHES buffer, pH9.5, 20% PEG8000 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2025 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.4→47.44 Å / Num. obs: 256392 / % possible obs: 91.4 % / Redundancy: 7 % / Biso Wilson estimate: 10.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 0.91 / Net I/σ(I): 15.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 4 / Num. unique obs: 7756 / CC1/2: 0.948 / Rpim(I) all: 0.153 / Rrim(I) all: 0.413 / Χ2: 0.52 / % possible all: 55.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.96 Å / SU ML: 0.1347 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 13112 5.11 %
Rwork0.1701 243252 -
obs0.1712 256364 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11534 0 2 1739 13275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006811965
X-RAY DIFFRACTIONf_angle_d0.939616202
X-RAY DIFFRACTIONf_chiral_restr0.08721773
X-RAY DIFFRACTIONf_plane_restr0.00852131
X-RAY DIFFRACTIONf_dihedral_angle_d13.34164478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2532460.20584801X-RAY DIFFRACTION54.27
1.42-1.430.25132520.20435388X-RAY DIFFRACTION60.07
1.43-1.450.22883390.1975848X-RAY DIFFRACTION66.69
1.45-1.470.24343500.19736783X-RAY DIFFRACTION76.04
1.47-1.490.21844450.19668091X-RAY DIFFRACTION91.04
1.49-1.510.21774550.18768332X-RAY DIFFRACTION94.31
1.51-1.530.23434510.17748401X-RAY DIFFRACTION94.42
1.53-1.550.2024290.17448350X-RAY DIFFRACTION94.26
1.55-1.580.19514190.17318370X-RAY DIFFRACTION94.33
1.58-1.60.20044260.1768462X-RAY DIFFRACTION94.42
1.6-1.630.20664270.17458395X-RAY DIFFRACTION94.45
1.63-1.660.20574470.1768417X-RAY DIFFRACTION94.81
1.66-1.690.20144340.17818444X-RAY DIFFRACTION94.98
1.69-1.730.21175080.17998387X-RAY DIFFRACTION95.18
1.73-1.760.21384310.18598446X-RAY DIFFRACTION95.21
1.76-1.80.22294570.19838463X-RAY DIFFRACTION95.3
1.8-1.850.2214660.18548469X-RAY DIFFRACTION95.61
1.85-1.90.21495010.18528465X-RAY DIFFRACTION95.8
1.9-1.960.19764730.17678485X-RAY DIFFRACTION95.81
1.96-2.020.20344690.17788547X-RAY DIFFRACTION95.91
2.02-2.090.20514420.17148503X-RAY DIFFRACTION96.11
2.09-2.170.18494410.16988543X-RAY DIFFRACTION96.34
2.17-2.270.20534680.16658541X-RAY DIFFRACTION96.44
2.27-2.390.18094410.16838605X-RAY DIFFRACTION96.62
2.39-2.540.20794140.17238659X-RAY DIFFRACTION96.83
2.54-2.740.20225350.17528532X-RAY DIFFRACTION96.91
2.74-3.020.19074680.17388573X-RAY DIFFRACTION97.12
3.02-3.450.17994720.16978635X-RAY DIFFRACTION97.17
3.45-4.350.15714870.14868679X-RAY DIFFRACTION97.99
4.35-40.960.1415190.13638638X-RAY DIFFRACTION98.09
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)
10.4426788279880.1884387848760.07777760816670.373578946063-0.04313859827820.33130916943-0.01260792111210.034405948160.0699050837868-0.005556302087370.00686929173095-0.0234265731121-0.05252161833860.0273681411540.01005870457240.0744405077526-0.003854441038780.008882371217510.0759270638554-0.001322856310230.080336376614444.68932170450.4726735514-0.0780950140509
21.40110789925-0.0746534588279-0.01377533013480.729840380288-0.1821944641951.26097114971-0.02240504924710.1013592467040.087708455682-0.0274789726374-0.02065493832340.0654080494136-0.0533150603042-0.07005910783420.02604282312040.0615809475210.00297372444774-0.006091005550820.072890926873-0.0009390754510560.07865139631989.7316242827341.7231982598-2.80724778591
30.455874386198-0.1722633705020.1354912607970.313050252839-0.03087604334690.210659712530.03852922741650.138386731692-0.0597415818103-0.0423038249226-0.03887313505290.005393540975320.03751668819330.0487410142158-0.0007515221459550.06754248792480.00167574118370.00208500267720.0960366080246-0.01840125762650.058021833455828.831701017722.0032947362-4.06509600427
40.360784501979-0.126085790215-0.04823085679260.368844783416-0.09041859633250.427055159653-0.0239206332236-0.0261701862644-0.07281426337860.00354686239961-0.00336349996451-0.03389639415420.07050209667290.03704192261410.02955118072730.069386814077-7.754814555E-50.005352159989290.06964727539030.001830137759040.087069364544.24647313464.2340751239931.7487827318
51.778410522020.527327391043-0.4246345700121.09111994501-0.06312851299081.651984483110.0181500697081-0.07908837043040.1098308256660.106153372284-0.04582629490870.179762529062-0.0984446437133-0.1800709920380.03059085740970.06287987468780.0168178224308-0.006788127655320.1324170780030.003266378544960.044401324034712.936735924520.804145549641.376968037
60.3893430002090.141343127675-0.008919620140530.315523038397-0.007793793093550.271523625432-0.00301442828459-0.07199685979520.02734091543450.0282143347186-0.01173225277510.0158012914027-0.0193217920497-0.01341201479760.01486378149620.06650014541790.01202266335070.004174332742770.0786598541793-0.01278651424460.061017778813725.059639657928.3633561835.3712543133
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 35 through 399 )AA35 - 3991 - 365
22chain 'A' and (resid 400 through 528 )AA400 - 528366 - 494
33chain 'A' and (resid 529 through 779 )AA529 - 779495 - 745
44chain 'B' and (resid 35 through 399 )BB35 - 3991 - 365
55chain 'B' and (resid 400 through 448 )BB400 - 448366 - 414
66chain 'B' and (resid 449 through 779 )BB449 - 779415 - 745

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