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- PDB-3qom: Crystal structure of 6-phospho-beta-glucosidase from Lactobacillu... -

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Basic information

Entry
Database: PDB / ID: 3qom
TitleCrystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum
Components6-phospho-beta-glucosidase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Glycoside hydrolase
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
ACETATE ION / beta-D-glucopyranose / PHOSPHATE ION / 6-phospho-beta-glucosidase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.498 Å
AuthorsMichalska, K. / Hatzos-Skintges, C. / Bearden, J. / Kohler, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.D / 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
DepositionFeb 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4247
Polymers55,8051
Non-polymers6196
Water10,629590
1
A: 6-phospho-beta-glucosidase
hetero molecules

A: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,84914
Polymers111,6112
Non-polymers1,23812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5340 Å2
ΔGint-35 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.647, 150.647, 95.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-482-

PO4

21A-484-

ACT

31A-484-

ACT

41A-507-

HOH

51A-769-

HOH

61A-947-

HOH

71A-981-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein 6-phospho-beta-glucosidase


Mass: 55805.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: pbg1, lp_0440 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: Q88ZA9, UniProt: F9UU25*PLUS, 6-phospho-beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 0.8 M NaH2PO4/1.2 M K2HPO4, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 102436 / Num. obs: 102382 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 33.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5046 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: dev_601)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.498→31.048 Å / SU ML: 0.16
Isotropic thermal model: anisotropic for protein atoms, isotropic for solvent
Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 10.59 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1341 1031 1.01 %RANDOM
Rwork0.1183 ---
all0.1184 102345 --
obs0.1184 102345 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.72 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2198 Å2-0 Å2-0 Å2
2--0.2198 Å20 Å2
3----0.4396 Å2
Refinement stepCycle: LAST / Resolution: 1.498→31.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 36 590 4508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154148
X-RAY DIFFRACTIONf_angle_d1.4555647
X-RAY DIFFRACTIONf_dihedral_angle_d13.3241497
X-RAY DIFFRACTIONf_chiral_restr0.095571
X-RAY DIFFRACTIONf_plane_restr0.009745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4975-1.57650.21651500.187114119X-RAY DIFFRACTION99
1.5765-1.67520.15331400.124814342X-RAY DIFFRACTION100
1.6752-1.80460.12681560.091614348X-RAY DIFFRACTION100
1.8046-1.98610.1371400.097114402X-RAY DIFFRACTION100
1.9861-2.27350.14971370.113714466X-RAY DIFFRACTION100
2.2735-2.8640.14421400.115414601X-RAY DIFFRACTION100
2.864-31.05490.11111680.123515036X-RAY DIFFRACTION100

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