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- PDB-9urg: Crystal structure of beta-glucosidase from Bacteroides ovatus bou... -

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Basic information

Entry
Database: PDB / ID: 9urg
TitleCrystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose
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
beta-D-glucopyranose / Periplasmic beta-glucosidase
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKumar, A.K. / Jamdar, S.N. / Sarver, R. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Crystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose
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)180,1676
Polymers179,7582
Non-polymers4094
Water22,0321223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-19 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.833, 74.965, 87.009
Angle α, β, γ (deg.)72.856, 67.761, 64.840
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 35 through 180 or resid 182...
d_2ens_1(chain "B" and (resid 35 through 180 or resid 182...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA35 - 18071 - 216
d_12GLYGLYLYSLYSAA112 - 204148 - 240
d_13METMETGLYGLYAA206 - 285242 - 321
d_14TRPTRPLYSLYSAA287 - 556323 - 592
d_15THRTHRASNASNAA628 - 779664 - 815
d_21SERSERSERSERBB35 - 18071 - 216
d_22GLYGLYLYSLYSBB112 - 204148 - 240
d_23METMETGLYGLYBB206 - 285242 - 321
d_24TRPTRPLYSLYSBB287 - 556323 - 592
d_25THRTHRASNASNBB628 - 779664 - 815

NCS oper: (Code: givenMatrix: (0.99577548024, -0.0683733837446, -0.061288443835), (-0.0680701475788, -0.997655808218, 0.0070244812582), (-0.0616250595213, -0.0028228927816, -0.998095377865)Vector: -3. ...NCS oper: (Code: given
Matrix: (0.99577548024, -0.0683733837446, -0.061288443835), (-0.0680701475788, -0.997655808218, 0.0070244812582), (-0.0616250595213, -0.0028228927816, -0.998095377865)
Vector: -3.26315257406, -63.3268550548, -38.8636777965)

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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 not removed
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_03380 / Plasmid: pSTSTRHisN / Details (production host): PST44 system from the Tan Lab / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0AAN3A6K2, 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: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 9.5
Details: 0.1 M CHES buffer, pH 9.5, 30% PEG8000 Full-grown soaked in crystallization drop containing approx 0.1 M Dextrose for 30 min
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 7, 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: 1.95→47.61 Å / Num. obs: 102129 / % possible obs: 97.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.073 / Rrim(I) all: 0.172 / Χ2: 1.02 / Net I/σ(I): 9.7
Reflection shellResolution: 1.95→1.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5043 / CC1/2: 0.802 / Rpim(I) all: 0.313 / Rrim(I) all: 0.745 / Χ2: 0.96 / % possible all: 96.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.67 Å / SU ML: 0.2326 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.4994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 5289 5.18 %
Rwork0.2017 96777 -
obs0.2036 102066 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11534 0 26 1223 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003611828
X-RAY DIFFRACTIONf_angle_d0.698516012
X-RAY DIFFRACTIONf_chiral_restr0.04821756
X-RAY DIFFRACTIONf_plane_restr0.00572102
X-RAY DIFFRACTIONf_dihedral_angle_d15.07484422
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.539433302203 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.2791850.22743240X-RAY DIFFRACTION95.4
1.97-20.311610.23043135X-RAY DIFFRACTION96.4
2-2.020.26621940.22213188X-RAY DIFFRACTION96.13
2.02-2.050.26391610.21523185X-RAY DIFFRACTION96.43
2.05-2.070.28661700.21893218X-RAY DIFFRACTION96.36
2.07-2.10.2821760.21573215X-RAY DIFFRACTION96.75
2.1-2.130.26631720.21013189X-RAY DIFFRACTION96.22
2.13-2.160.27731520.2093249X-RAY DIFFRACTION96.81
2.16-2.20.24861700.20573194X-RAY DIFFRACTION96.47
2.2-2.230.2861680.19963189X-RAY DIFFRACTION96.72
2.23-2.270.23981850.20473218X-RAY DIFFRACTION96.79
2.27-2.310.28031780.21323194X-RAY DIFFRACTION96.76
2.31-2.360.27871590.21313232X-RAY DIFFRACTION96.61
2.36-2.40.2511670.21383229X-RAY DIFFRACTION97.08
2.4-2.460.29971640.2113231X-RAY DIFFRACTION97.11
2.46-2.510.27591500.21833259X-RAY DIFFRACTION97.32
2.51-2.580.28511680.21453232X-RAY DIFFRACTION97.28
2.58-2.650.25381810.21883214X-RAY DIFFRACTION97.47
2.65-2.720.25442150.21673159X-RAY DIFFRACTION97.46
2.72-2.810.24391730.21463257X-RAY DIFFRACTION97.64
2.81-2.910.25351820.21383240X-RAY DIFFRACTION97.94
2.91-3.030.26621820.21513247X-RAY DIFFRACTION97.97
3.03-3.170.26931840.21753227X-RAY DIFFRACTION97.96
3.17-3.330.23581620.21673272X-RAY DIFFRACTION98
3.33-3.540.23081760.20783265X-RAY DIFFRACTION98.12
3.54-3.820.2092090.19553264X-RAY DIFFRACTION98.41
3.82-4.20.19231640.1783272X-RAY DIFFRACTION98.4
4.2-4.810.17411790.15993251X-RAY DIFFRACTION98.62
4.81-6.050.17142070.16643245X-RAY DIFFRACTION99
6.05-38.670.17141950.16863267X-RAY DIFFRACTION98.75
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)
10.336504819976-0.110711404501-0.04671123385060.175999347725-0.04521416501870.229486829977-0.0332010732585-0.00595915020752-0.03920445902280.00241381526723-0.00169119439706-0.01234203765820.02786501491810.045136837519-0.03280461273290.07784881133420.005405962510680.005081191113980.0771457506860.00844342866490.0751335555675-28.3352766686-53.672266938-2.50368426639
20.07021117825840.04848470241360.04053385672170.09597562539310.01648502798630.117109029194-0.0137587350844-0.0563102570698-0.02591032376710.00336923492273-0.01442270928040.01509054989870.0144093451162-0.0464830515743-0.009181024764430.06868029020740.001843855598340.01160706310120.0869382346221-0.004530347432410.0771106233636-62.7172860679-42.82167870212.08689362204
30.044251741852-0.04216606894620.08908847732250.195912025397-0.09428097756310.154668486072-0.0147697380931-0.01084328559170.04491012005110.01501024297470.002845860906170.000655078699026-0.0534554760899-0.02037326773691.04051985089E-70.09054269097440.003069765634440.001833804065710.0771807872139-0.01630703047750.0700944366108-42.2803560145-24.51251684912.02461332408
40.3786469704760.0718331190090.002983214226460.191228795322-0.05761359200710.0749797218432-0.004209393053220.04975101413920.04522347632480.005058210506010.00122929540528-0.0243331063228-0.008698329166460.0187855155113-0.0006342904069090.0800761272454-0.004750061261990.002038214831410.0810942589260.01064303733310.0802296859298-27.6551427347-7.98041694994-34.5233101818
50.112341734696-0.107927979808-0.0275697159160.0719110358176-0.01170722213720.0747738619643-0.009023352343470.01171874055680.0408949014363-0.00472964287155-0.02814411016750.0370304765569-0.028709300304-0.0486730390586-0.005915774250160.0917338426338-0.00285756186313-0.01341742304210.0945691807756-0.005873052946370.0969947142331-62.9035139352-16.2822700727-36.9372274838
60.15248002825-0.09646000915590.05173122050160.176481438432-0.06116572934990.1345864825460.009374779087910.0268765003429-0.03680335182740.00280703408197-0.004190713907390.02565586721690.01474679629720.0166367401680.004561290854380.08224678763690.00268618772138-0.006782115514590.091039521908-0.0180892446960.0790081357541-43.747920356-36.0084092015-38.142287464
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 )BC35 - 3991 - 365
55chain 'B' and (resid 400 through 528 )BC400 - 528366 - 494
66chain 'B' and (resid 529 through 779 )BC529 - 779495 - 745

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