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- PDB-8u7f: Crystal structure of CIB_12 beta-galactosidase from Cuniculiplasm... -

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Basic information

Entry
Database: PDB / ID: 8u7f
TitleCrystal structure of CIB_12 beta-galactosidase from Cuniculiplasma divulgatum
ComponentsCIB_12 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: 2.55 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Yakunin, A. / Golyshin, P. / Savchenko, A.
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 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CIB_12 Beta-galactosidase
B: CIB_12 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9744
Polymers113,7902
Non-polymers1842
Water1,928107
1
A: CIB_12 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9872
Polymers56,8951
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CIB_12 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9872
Polymers56,8951
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.215, 51.805, 128.794
Angle α, β, γ (deg.)90.000, 108.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein CIB_12 Beta-galactosidase


Mass: 56894.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cuniculiplasma divulgatum (archaea) / Gene: CSP5_0942 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1N5UH46
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350 25%, 0.2 M sodium tartrate, 0.1 M Tris pH 8.5, 0.3 M NDSB 201, 1% 1-butyl-2,3-dimethylimidazolium tetrafluoroborate

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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: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→25 Å / Num. obs: 38156 / % possible obs: 95.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 50.04 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.047 / Net I/σ(I): 18.34
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1629 / CC1/2: 0.886 / Rpim(I) all: 0.289 / % possible all: 81.5

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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: 2.55→24.93 Å / SU ML: 0.3519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1902 5 %RANDOM
Rwork0.2198 36167 --
obs0.2217 38069 94.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.25 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 12 107 8043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288152
X-RAY DIFFRACTIONf_angle_d0.553311009
X-RAY DIFFRACTIONf_chiral_restr0.04611105
X-RAY DIFFRACTIONf_plane_restr0.00431418
X-RAY DIFFRACTIONf_dihedral_angle_d16.70392993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.35671120.32812130X-RAY DIFFRACTION78.75
2.61-2.680.32041240.30762352X-RAY DIFFRACTION87.31
2.68-2.760.33241300.29432468X-RAY DIFFRACTION91
2.76-2.850.32081350.28932569X-RAY DIFFRACTION95.11
2.85-2.950.3381370.28052603X-RAY DIFFRACTION96.48
2.95-3.070.38181380.27262619X-RAY DIFFRACTION96.43
3.07-3.210.31761360.27272628X-RAY DIFFRACTION96.54
3.21-3.380.33281380.25632611X-RAY DIFFRACTION97.03
3.38-3.590.30841390.24492634X-RAY DIFFRACTION97.03
3.59-3.860.24771380.21042643X-RAY DIFFRACTION97.27
3.86-4.250.21261410.18612684X-RAY DIFFRACTION97.89
4.25-4.860.19871420.16342686X-RAY DIFFRACTION98.06
4.86-6.110.23391430.18822731X-RAY DIFFRACTION98.56
6.11-24.930.21671490.19612809X-RAY DIFFRACTION98.34
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)
13.05883888570.383253860598-0.3167048185681.35869886144-0.3201007207441.78567888580.01981136548180.2756805651070.0530741143126-0.09181175737650.0822081339467-0.161367139831-0.2337464791990.591949181007-0.1030157933480.413539975884-0.112376455906-0.03005406297050.551557407654-0.009673605586770.31683965246217.397459938-23.3629741616.99131397315
22.41057378229-0.3607293486040.174479100051.58111091714-0.2633861828691.994664758240.1298763868040.0243238689336-0.0692987906545-0.03477269097585.83909616793E-5-0.211027483627-0.4327483810350.789942735723-0.1151168914680.527580435039-0.2281871298010.006593821550770.799584203731-0.04169425325860.46119139349826.3674134493-21.475136311511.7310603405
37.049034888040.152117031022-1.146699579271.35630896502-0.6477229854031.55635220866-0.013241183862-0.819593373506-0.03327264299730.0799905663487-0.0278179716241-0.519207073329-0.3170381125751.44881628345-0.007582126562040.536918277837-0.263657519018-0.02327798546881.49397308132-0.01004884667420.71633974730141.1310460672-23.178801115619.97825733
42.259693755140.0713920990426-0.5640336035790.9926133928270.2203771076172.36216581280.0695785095297-0.477754735234-0.07990508862560.222328883315-0.0205897630786-0.256365333597-0.07273448322910.385337169481-0.04203569180810.367351403806-0.0717039791821-0.0245369376150.568029248090.03854660796460.36004715533812.1983561838-30.232035024626.348100626
51.513529749621.06812668498-0.7748401401110.680169380107-0.4044851759325.091040162520.188568411042-0.328197009437-0.1342668109950.225406189447-0.2014861579860.0103618606908-0.1344107459820.01485759061730.009694405907330.3748854071170.1009470405270.01435922997160.6356737166740.01329571218520.385186087871-21.8994709544-35.476784816845.6501359577
62.077703142870.877453556043-0.5452459897821.2318858262-0.2557525439451.775115824610.188512281461-0.4802229535820.2130602764670.115231957036-0.07582562291240.272479771993-0.0290153592142-0.503261648265-0.1278498090760.4066059302670.0934800669819-0.003329257685350.817161210767-0.03219611138640.395902705357-31.1239921513-28.958963439948.86752209
72.725759993510.31281907329-1.046215020884.39833963466-1.149566500074.60383119080.302995328044-0.383913712833-0.1420533546420.2460877289150.06161700166430.4081119717730.0415311983879-0.483637337488-0.3633504592870.3639056189660.00178782308879-0.01576749285920.797890984929-0.01521491951820.389538873318-31.3159926838-38.17533412347.541792178
80.8412264885720.149195857256-0.6231863983281.401648934630.332173959012.428888609710.141354539771-0.182560526537-0.107230646593-0.0657136668394-0.1250682742810.3511014184940.0910905801741-0.9124445605850.02138825170230.41935962-0.00232414506887-0.07677794849041.037448033340.01501138745140.5570618072-37.0892466463-40.604959810637.5702778699
97.76912023022-0.293965453991-1.460877559073.16908584616-0.3957251404590.7046681608530.0451838643826-0.0304008181122-0.513996581069-0.448982511428-0.03156851053010.5526689357610.55077781982-1.19238428211-0.1013420282630.491068459145-0.167980421453-0.1026449508791.40818998894-0.06390758231540.566538450352-47.0783146217-46.193342526933.8836086181
102.81198639206-2.37393176896-0.5349425714577.433948421112.084571087345.252358423630.1259450066490.13555568116-0.285337264520.162458862209-0.241380198790.1843019244940.435599967365-0.4573364268810.1221192474570.4446258108-0.0497247017604-0.08094633803140.6348819051590.01222915979680.364396867933-26.5846325513-51.307026581627.9193261281
111.184416973080.2624620060130.2609950137951.221500816490.3126460099982.824350280950.0179569950246-0.0646000814567-0.0964016052053-0.1326403551720.03138979843250.0295169815046-0.0126293782782-0.168171063317-0.05969597060120.298302092160.02441863524910.0005069464105260.5336746063590.008587682178830.33373008774-16.8807449371-36.175367780828.1673849317
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 109 )AA1 - 1091 - 109
22chain 'A' and (resid 110 through 274 )AA110 - 274110 - 268
33chain 'A' and (resid 275 through 314 )AA275 - 314269 - 308
44chain 'A' and (resid 315 through 484 )AA315 - 484309 - 478
55chain 'B' and (resid 1 through 41 )BB1 - 411 - 41
66chain 'B' and (resid 42 through 138 )BB42 - 13842 - 138
77chain 'B' and (resid 139 through 174 )BB139 - 174139 - 167
88chain 'B' and (resid 175 through 274 )BB175 - 274168 - 267
99chain 'B' and (resid 275 through 314 )BB275 - 314268 - 307
1010chain 'B' and (resid 315 through 339 )BB315 - 339308 - 332
1111chain 'B' and (resid 340 through 484 )BB340 - 484333 - 477

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