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- PDB-4f79: The crystal structure of 6-phospho-beta-glucosidase mutant (E375Q... -

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Basic information

Entry
Database: PDB / ID: 4f79
TitleThe crystal structure of 6-phospho-beta-glucosidase mutant (E375Q) in complex with Salicin 6-phosphate
ComponentsPutative phospho-beta-glucosidase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / carbohydrate catabolic process / cytosol
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
Chem-P53 / Phospho-beta-glucosidase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTan, K. / Michalska, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
Authors: Michalska, K. / Tan, K. / Li, H. / Hatzos-Skintges, C. / Bearden, J. / Babnigg, G. / Joachimiak, A.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0254
Polymers55,4741
Non-polymers5503
Water61334
1
A: Putative phospho-beta-glucosidase
hetero molecules

A: Putative phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0508
Polymers110,9492
Non-polymers1,1016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4550 Å2
ΔGint-23 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.278, 82.278, 221.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsIt is predicted to be monomer.

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Components

#1: Protein Putative phospho-beta-glucosidase


Mass: 55474.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: bgl, SMU_1601 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8DT00, 6-phospho-beta-glucosidase
#2: Sugar ChemComp-P53 / 2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucopyranoside / Salicin-6-phosphate / 2-(hydroxymethyl)phenyl 6-O-phosphono-beta-D-glucoside / 2-(hydroxymethyl)phenyl 6-O-phosphono-D-glucoside / 2-(hydroxymethyl)phenyl 6-O-phosphono-glucoside


Type: D-saccharide / Mass: 366.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H19O10P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES:NaOH, 25% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.54→39 Å / Num. all: 25874 / Num. obs: 25874 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.8
Reflection shellResolution: 2.54→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1278 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 3PN8

3pn8


Resolution: 2.54→38.966 Å / SU ML: 0.63 / σ(F): 1.33 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1312 5.09 %random
Rwork0.1803 ---
obs0.1826 25791 99.24 %-
all-25791 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.872 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.5427 Å20 Å2-0 Å2
2--7.5427 Å20 Å2
3----15.0855 Å2
Refinement stepCycle: LAST / Resolution: 2.54→38.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 36 34 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074054
X-RAY DIFFRACTIONf_angle_d1.0585489
X-RAY DIFFRACTIONf_dihedral_angle_d16.8431457
X-RAY DIFFRACTIONf_chiral_restr0.071549
X-RAY DIFFRACTIONf_plane_restr0.004710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.64140.34411420.25832620X-RAY DIFFRACTION98
2.6414-2.76150.26881370.22862679X-RAY DIFFRACTION100
2.7615-2.90710.29811450.22122683X-RAY DIFFRACTION100
2.9071-3.08920.27381470.22222688X-RAY DIFFRACTION100
3.0892-3.32760.28741660.20732694X-RAY DIFFRACTION100
3.3276-3.66220.21411450.19292708X-RAY DIFFRACTION100
3.6622-4.19160.22761400.15292740X-RAY DIFFRACTION99
4.1916-5.27890.18661350.14062772X-RAY DIFFRACTION99
5.2789-38.97070.1991550.17932895X-RAY DIFFRACTION98
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)
12.5135-1.4246-0.47654.4234-0.47253.1803-0.03160.0755-0.2398-0.1206-0.1979-0.4420.77360.43220.19640.52360.0277-0.14270.3910.04450.390934.2563-4.841913.7196
22.0804-0.36390.09293.25980.54173.00820.2859-0.114-0.42950.0276-0.2283-0.3151.33490.3158-0.09190.7993-0.0031-0.20450.47220.15690.434632.355-13.643618.3255
31.7766-0.28231.57282.2524-1.42761.96780.3633-0.006-0.3174-0.4949-0.4675-0.20911.75040.91070.15561.05540.0596-0.0580.31630.05210.433427.8074-10.06992.9831
41.55240.10910.73682.3397-1.1843.02540.23910.069-0.0802-0.4395-0.17940.08260.82820.0222-0.02380.4518-0.0589-0.06680.30690.02370.324421.11032.6029-1.1384
55.72150.1971-1.58244.4027-0.74944.604-0.0090.3692-0.235-0.8280.00920.30670.9531-0.54320.0110.8252-0.0876-0.17060.3970.0280.372117.1338-2.1954-12.0517
60.6407-0.05661.00832.2996-1.24555.2937-0.05720.19310.1807-0.1153-0.2382-0.51850.00620.76020.27510.35020.0152-0.03230.52290.13570.538431.051513.30121.0916
71.8437-1.1687-0.05322.6378-0.78343.0529-0.0509-0.40540.19520.4567-0.162-0.60110.14750.50020.1860.4454-0.1314-0.14010.43970.06890.441230.50147.006420.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:50)
2X-RAY DIFFRACTION2chain 'A' and (resseq 51:120)
3X-RAY DIFFRACTION3chain 'A' and (resseq 121:202)
4X-RAY DIFFRACTION4chain 'A' and (resseq 203:272)
5X-RAY DIFFRACTION5chain 'A' and (resseq 273:302)
6X-RAY DIFFRACTION6chain 'A' and (resseq 303:352)
7X-RAY DIFFRACTION7chain 'A' and (resseq 353:477)

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