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- PDB-7m1r: Crystal structure of a 6-phospho-beta-galactosidase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 7m1r
TitleCrystal structure of a 6-phospho-beta-galactosidase from Bacillus licheniformis
Components6-phospho-beta-galactosidase
KeywordsHYDROLASE / 6-phospho-beta-galactosidase / GH1 / bacillus licheniformis
Function / homology
Function and homology information


cellulase / cellulase activity / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 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: 2021
Title: Differences in Gluco and Galacto Substrate-Binding Interactions in a Dual 6P beta-Glucosidase/6P beta-Galactosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis .
Authors: Veldman, W. / Liberato, M.V. / Souza, V.P. / Almeida, V.M. / Marana, S.R. / Tastan Bishop, O. / Polikarpov, I.
History
DepositionMar 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)223,10214
Polymers222,4814
Non-polymers62110
Water28,3561574
1
A: 6-phospho-beta-galactosidase
hetero molecules

D: 6-phospho-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4896
Polymers111,2412
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area3870 Å2
ΔGint3 kcal/mol
Surface area31600 Å2
MethodPISA
2
B: 6-phospho-beta-galactosidase
hetero molecules

C: 6-phospho-beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6138
Polymers111,2412
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4460 Å2
ΔGint11 kcal/mol
Surface area32610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.988, 71.380, 169.290
Angle α, β, γ (deg.)90.000, 100.940, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAuthors stated the biological assembly is unknown

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Components

#1: Protein
6-phospho-beta-galactosidase / / Cellulase


Mass: 55620.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: bglC1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G1GM07, cellulase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1574 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 15% PEG4000, 0.2 M sodium acetate, and 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9765 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: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.98→98.17 Å / Num. obs: 155511 / % possible obs: 94.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.069 / Rrim(I) all: 0.115 / Net I/σ(I): 6.6 / Num. measured all: 368584 / Scaling rejects: 92
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
1.98-2.012.50.3751901277090.80.2720.4662.695.6
10.82-98.172.60.097265310400.6980.0790.12612.495.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.16 Å78.27 Å
Translation4.16 Å78.27 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
iMOSFLM7.3.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZEN

4zen


Resolution: 1.98→65.59 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 7915 5.09 %
Rwork0.1552 147531 -
obs0.1569 155446 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.51 Å2 / Biso mean: 34.0369 Å2 / Biso min: 10.76 Å2
Refinement stepCycle: final / Resolution: 1.98→65.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15200 0 40 1574 16814
Biso mean--31.39 39.1 -
Num. residues----1896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-20.24732720.21314925519795
2-2.020.2412770.19454900517795
2.02-2.050.23512850.19044973525895
2.05-2.070.22262550.18954855511095
2.07-2.10.24642660.18794960522695
2.1-2.130.23562610.17824905516695
2.13-2.160.22172810.17674885516695
2.16-2.190.22682320.17444909514194
2.19-2.220.21032600.174859511994
2.22-2.260.24192720.16784720499292
2.26-2.30.2182620.1664879514194
2.3-2.340.19242640.1574922518696
2.34-2.390.20152610.15485013527495
2.39-2.440.2152480.1584958520696
2.44-2.490.18822550.15334957521295
2.49-2.550.21572660.15534916518295
2.55-2.610.21122790.1564883516294
2.61-2.680.19872760.1534826510293
2.68-2.760.19872230.15654841506492
2.76-2.850.19812480.15274965521395
2.85-2.950.20662700.15764970524096
2.95-3.070.18462500.15264991524195
3.07-3.210.17732620.15554949521195
3.21-3.380.19162400.16284991523195
3.38-3.590.16912650.14894856512193
3.59-3.870.16882780.14394968524695
3.87-4.250.1542420.12815010525295
4.25-4.870.14452920.12464922521495
4.87-6.130.16292870.14624867515492
6.14-65.590.18542860.17094956524291
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)
10.9078-0.0092-0.01280.999-0.05630.8827-0.0572-0.0957-0.1390.20180.02520.21990.055-0.06670.01530.2108-0.00060.03360.12180.03670.2661-40.416641.5795-36.8429
21.54310.173-0.1490.7407-0.10040.62140.0460.21650.0275-0.0539-0.00090.075-0.0571-0.0297-0.03290.13190.0075-0.01180.12480.00740.1127-19.02229.6674-64.2687
31.3853-0.1820.15680.9389-0.10630.79970.05870.18030.08460.0228-0.12-0.1694-0.03620.25250.03740.138-0.0418-0.00070.25970.04960.1358-72.68997.5135-65.0218
41.16350.25440.18890.9337-0.01041.1946-0.06010.35660.0846-0.3522-0.0770.1202-0.0268-0.21060.11740.62710.02650.10420.4757-0.11440.3953-706.5736-8.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 478)A4 - 478
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 502)B2 - 502
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 477)C6 - 477
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 477)D6 - 477

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