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- PDB-6wgd: Crystal structure of a 6-phospho-beta-glucosidase from Bacillus l... -

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Basic information

Entry
Database: PDB / ID: 6wgd
TitleCrystal structure of a 6-phospho-beta-glucosidase from Bacillus licheniformis
Components6-phospho-beta-glucosidase
KeywordsHYDROLASE / 6-phospho-beta-glucosidase / GH1 / bacillus licheniformis
Function / homology
Function and homology information


: / 6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
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
6-phospho-beta-glucosidase / Beta-glucosidase, Glycoside Hydrolase Family 1
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLiberato, M.V. / Popov, A. / Polikarpov, I.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)423693/2016-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303988/2016-9 Brazil
CitationJournal: J.Chem.Inf.Model. / Year: 2020
Title: X-ray Structure, Bioinformatics Analysis, and Substrate Specificity of a 6-Phospho-beta-glucosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis .
Authors: Veldman, W. / Liberato, M.V. / Almeida, V.M. / Souza, V.P. / Frutuoso, M.A. / Marana, S.R. / Moses, V. / Tastan Bishop, O. / Polikarpov, I.
History
DepositionApr 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phospho-beta-glucosidase
B: 6-phospho-beta-glucosidase
C: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6708
Polymers160,3603
Non-polymers3105
Water8,089449
1
A: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5152
Polymers53,4531
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5773
Polymers53,4531
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5773
Polymers53,4531
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.272, 98.272, 285.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 6-phospho-beta-glucosidase


Mass: 53453.184 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: ascB, GII88_21755 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5Q3BW14, UniProt: Q65D37*PLUS, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG4000, 0.1 M ammonium sulphate, and 0.1 M Tris, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→49.14 Å / Num. obs: 82240 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.065 / Rrim(I) all: 0.153 / Net I/σ(I): 7.7 / Num. measured all: 456034 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.245.71.542565544850.860.7041.6961.599.8
11.43-49.144.70.06732956970.9970.0330.07620.498.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.25 Å48.43 Å
Translation4.25 Å48.43 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IPL

4ipl


Resolution: 2.2→48.425 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2441 4077 4.97 %
Rwork0.21 --
obs0.2117 81976 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.65 Å2 / Biso mean: 51.1029 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 2.2→48.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10631 0 20 449 11100
Biso mean--51.77 46.95 -
Num. residues----1358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.22590.33931170.3508263699
2.2259-2.2530.39611340.3289267099
2.253-2.28150.39091680.32772636100
2.2815-2.31160.35521530.3091260799
2.3116-2.34320.36061520.3072666100
2.3432-2.37670.34261480.299258899
2.3767-2.41220.32531560.2878263099
2.4122-2.44990.36091370.28862669100
2.4499-2.490.30271430.28572637100
2.49-2.5330.33751340.276267299
2.533-2.5790.3231330.27372706100
2.579-2.62860.29821370.25652621100
2.6286-2.68230.3221280.2506267999
2.6823-2.74060.28171220.24712673100
2.7406-2.80430.28231540.24042659100
2.8043-2.87450.27961510.23012651100
2.8745-2.95220.3224940.22662730100
2.9522-3.0390.26531450.22992657100
3.039-3.13710.25341420.2362680100
3.1371-3.24920.31911420.23232705100
3.2492-3.37930.24671260.21722687100
3.3793-3.5330.22961340.20652705100
3.533-3.71920.2141580.19162681100
3.7192-3.95210.20521520.17712719100
3.9521-4.25710.191420.16482745100
4.2571-4.68520.16381340.14612725100
4.6852-5.36240.17871400.15972754100
5.3624-6.75320.20971490.18762773100
6.7532-48.4250.22931520.1796293899
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)
11.47050.3716-0.17581.370.20011.49140.20090.17810.1725-0.0474-0.06310.0176-0.2819-0.0141-0.12330.4570.06230.10750.49630.04140.35224.915613.244116.3889
26.1644-0.3231.98531.30640.30453.967-0.0019-0.3187-0.01440.11550.085-0.0404-0.54820.1109-0.08790.4484-0.00140.12420.4213-0.01620.344710.34114.539827.7536
31.1966-0.2665-0.51441.38770.15033.47880.1746-0.16060.11240.1195-0.0031-0.0182-0.14080.5455-0.17580.46240.01960.1110.6083-0.02790.40397.706411.642740.3377
41.2426-0.197-0.88330.47920.91174.00280.07350.0076-0.09190.11990.03570.02450.3605-0.0127-0.11170.39280.03580.02250.39820.03110.3319-0.9374-3.064523.8964
51.4497-0.3705-0.14480.982-0.26661.15580.1405-0.2370.14930.4382-0.11430.0852-0.56220.1098-0.01720.9104-0.06890.09570.4864-0.0320.312143.960135.803957.1813
62.4840.23970.08861.3507-0.28992.43540.1680.11180.26640.3453-0.12960.2704-0.6227-0.1844-0.03460.77340.08730.15280.3641-0.00530.377337.672742.631143.8181
70.2537-0.20770.22592.46731.62033.6669-0.03540.0677-0.0218-0.00830.06890.0619-0.41860.229-0.02820.478-0.00190.06790.4933-0.00250.31543.592828.850129.6322
80.8857-0.2360.42111.7610.56651.61060.03830.16370.10310.0735-0.10310.1725-0.459-0.11510.05730.45260.06240.09770.54750.04780.324538.835936.237229.3597
96.64511.17260.7951.1943-0.14222.19120.0771-1.2253-0.88270.2263-0.11090.09330.6066-0.67580.08550.6345-0.01670.0890.66720.08480.485637.939610.162335.1262
101.22540.321-0.3830.8819-0.54183.19180.1534-0.087-0.08920.3058-0.1451-0.01070.08440.3943-0.00210.57430.0056-0.0130.4321-0.0010.309352.703421.670248.9438
111.3567-0.34280.04221.9464-0.19752.6459-0.032-0.43370.08360.21330.01830.0986-0.5256-0.34240.03260.54650.086-0.00580.7258-0.01920.302146.6098-18.06569.7179
123.823-0.29270.49071.7916-0.88994.1537-0.1374-0.17880.2601-0.11260.15670.1405-0.7613-0.5363-0.00740.64970.1288-0.00330.4687-0.03460.309244.9513-10.3052-3.4725
131.37261.97341.28924.59222.26373.2633-0.09910.12290.0868-0.00450.03920.1875-0.12560.23510.04010.47830.04390.02230.4538-0.01530.298743.822-24.7284-15.9028
141.22950.68270.38112.61550.4631.7905-0.0257-0.01060.05260.1006-0.01510.2374-0.2882-0.22050.03610.42980.13170.02120.5054-0.0210.28439.6311-23.7715-13.7774
151.82790.3009-0.31760.5445-0.23374.16630.044-0.4007-0.29350.0919-0.0297-0.01610.45430.08320.00510.45450.099-0.01720.47870.04830.345648.8938-35.70712.933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 162 )A4 - 162
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 196 )A163 - 196
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 289 )A197 - 289
4X-RAY DIFFRACTION4chain 'A' and (resid 290 through 469 )A290 - 469
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 119 )B5 - 119
6X-RAY DIFFRACTION6chain 'B' and (resid 120 through 222 )B120 - 222
7X-RAY DIFFRACTION7chain 'B' and (resid 223 through 266 )B223 - 266
8X-RAY DIFFRACTION8chain 'B' and (resid 267 through 315 )B267 - 315
9X-RAY DIFFRACTION9chain 'B' and (resid 316 through 346 )B316 - 346
10X-RAY DIFFRACTION10chain 'B' and (resid 347 through 469 )B347 - 469
11X-RAY DIFFRACTION11chain 'C' and (resid 4 through 145 )C4 - 145
12X-RAY DIFFRACTION12chain 'C' and (resid 146 through 222 )C146 - 222
13X-RAY DIFFRACTION13chain 'C' and (resid 223 through 266 )C223 - 266
14X-RAY DIFFRACTION14chain 'C' and (resid 267 through 345 )C267 - 345
15X-RAY DIFFRACTION15chain 'C' and (resid 346 through 469 )C346 - 469

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