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- PDB-8u7g: Crystal structure of CIB_13 beta-galactosidase from Cuniculiplasm... -

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Basic information

Entry
Database: PDB / ID: 8u7g
TitleCrystal structure of CIB_13 beta-galactosidase from Cuniculiplasma divulgatum
ComponentsCIB_13 Beta-galactosidase
KeywordsHYDROLASE / beta-galactosidase
Function / homology: / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Beta-galactosidase
Function and homology information
Biological speciesCuniculiplasma divulgatum (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsStogios, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Fems Microbiol.Ecol. / Year: 2024
Title: Moderately thermostable GH1 beta-glucosidases from hyperacidophilic archaeon Cuniculiplasma divulgatum S5.
Authors: Khusnutdinova, A.N. / Tran, H. / Devlekar, S. / Distaso, M.A. / Kublanov, I.V. / Skarina, T. / Stogios, P. / Savchenko, A. / Ferrer, M. / Golyshina, O.V. / Yakunin, A.F. / Golyshin, P.N.
History
DepositionSep 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CIB_13 Beta-galactosidase
B: CIB_13 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7514
Polymers112,5372
Non-polymers2142
Water12,034668
1
A: CIB_13 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3612
Polymers56,2681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CIB_13 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3912
Polymers56,2681
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.800, 102.188, 97.542
Angle α, β, γ (deg.)90.000, 104.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein CIB_13 Beta-galactosidase


Mass: 56268.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cuniculiplasma divulgatum (archaea) / Gene: CSP5_1651 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1N5W3X4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 25% PEG 3350, 0.2 M KCl, 0.1 M Tris 0.1 pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. obs: 49087 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.86 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.036 / Net I/σ(I): 16.89
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 2010 / CC1/2: 0.875 / Rpim(I) all: 0.215 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→29.63 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2007 4.09 %RANDOM
Rwork0.1794 47047 --
obs0.1811 49054 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.65 Å2
Refinement stepCycle: LAST / Resolution: 2.22→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 14 668 8610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218156
X-RAY DIFFRACTIONf_angle_d0.497810972
X-RAY DIFFRACTIONf_chiral_restr0.04181091
X-RAY DIFFRACTIONf_plane_restr0.00311418
X-RAY DIFFRACTIONf_dihedral_angle_d15.78953047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.260.34181040.26132654X-RAY DIFFRACTION76.93
2.26-2.320.31631360.24793140X-RAY DIFFRACTION91.74
2.32-2.390.28671410.23153326X-RAY DIFFRACTION96.65
2.39-2.470.2541390.22833395X-RAY DIFFRACTION99.49
2.47-2.560.27231470.22373452X-RAY DIFFRACTION99.92
2.56-2.660.27711490.21393427X-RAY DIFFRACTION99.89
2.66-2.780.26671500.21733442X-RAY DIFFRACTION99.89
2.78-2.930.27471450.20813448X-RAY DIFFRACTION99.92
2.93-3.110.26711490.19623447X-RAY DIFFRACTION99.94
3.11-3.350.23161450.19333423X-RAY DIFFRACTION99.92
3.35-3.690.20991510.17073443X-RAY DIFFRACTION99.97
3.69-4.220.19871520.14443455X-RAY DIFFRACTION99.94
4.22-5.310.1531440.13123488X-RAY DIFFRACTION100
5.31-29.630.1611550.15523507X-RAY DIFFRACTION99.84
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)
11.26642602067-0.5793299533920.0569444528732.913685742110.6651434045570.898055824052-0.0337027375787-0.07880037660170.1852172482910.119160647918-0.06819925554840.309805010029-0.00523820960595-0.16831481470.09854732842990.1974241320310.01905342658480.03205898030860.310224892645-0.03765496093110.26481340946831.026370096123.210995195231.7429725281
22.38776360341-0.352686266414-0.6414948849981.828384401080.426301762081.952086608610.09441041789840.1289386085950.450599998671-0.265026847583-0.0499213214198-0.0621874779246-0.376711688316-0.146392038518-0.03637857729010.272811745540.03657937350190.00868021472090.225772587570.01365379612390.34070100666839.504637793635.604694271420.8852895108
31.79463852261.2999715241-0.6252126584452.01859842754-0.8641488508952.372124858170.0391256370580.5188193908210.020786543128-0.5913607628770.0766889192868-0.01986862795790.120590995621-0.292665458505-0.07924227259910.4242882758190.03999779909090.05128613468860.402207591470.03307369040110.29198257391449.20265893219.02723869136.22505401677
41.28067771602-0.217673221199-0.4068527338451.88872532926-0.01850451502780.809572135886-0.0602752508375-0.1261168116110.1166890941560.02422571006910.0804596044278-0.3165699150780.02540573768970.0949327592025-0.02248102439880.2088014573110.0231135347890.008250134768430.273504046041-0.01143740621390.27471628155150.148327539413.564731676725.4060298552
51.09869315868-0.0607109850731-0.09352364865411.35687334114-0.1028291103771.204226493330.115262997761-0.0252950944715-0.283582736869-0.08791253781310.06580872158020.2058849361430.176605305094-0.239371238209-0.1488659581830.251081602715-0.0537898131015-0.07975763654880.2789987477740.03160407189510.3474659890947.0424236491728.053060217165.6567661525
61.167181891870.05589171623960.2555411871161.00771825293-0.03535146286280.8357160074540.114122514583-0.039335621661-0.3068128550050.03394110876070.04844461495680.005307667068770.1910649143690.0242693041008-0.1601226400740.257090740438-0.00383932746204-0.03173364685340.2371689472930.01126822094170.31842024155323.894255692525.1626628471.1415528897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 155 )AA0 - 1551 - 156
22chain 'A' and (resid 156 through 321 )AA156 - 321157 - 322
33chain 'A' and (resid 322 through 362 )AA322 - 362323 - 363
44chain 'A' and (resid 363 through 481 )AA363 - 481364 - 482
55chain 'B' and (resid 0 through 160 )BB0 - 1601 - 161
66chain 'B' and (resid 161 through 481 )BB161 - 481162 - 482

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