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- PDB-4ipn: The complex structure of 6-phospho-beta-glucosidase BglA-2 with t... -

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Basic information

Entry
Database: PDB / ID: 4ipn
TitleThe complex structure of 6-phospho-beta-glucosidase BglA-2 with thiocellobiose-6P from Streptococcus pneumoniae
Components6-phospho-beta-glucosidase
KeywordsHYDROLASE / Hydrolysase
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / methyl beta-D-glucoside 6-phosphate glucohydrolase 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
thio-alpha-cellobiose 6-phosphate / 6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å
AuthorsYu, W.L. / Jiang, Y.L. / Andreas, P. / Cheng, W. / Bai, X.H. / Ren, Y.M. / Thompsonn, J. / Zhou, C.Z. / Chen, Y.X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural insights into the substrate specificity of a 6-phospho-&[beta]-glucosidase BglA-2 from Streptococcus pneumoniae TIGR4
Authors: Yu, W.L. / Jiang, Y.L. / Pikis, A. / Cheng, W. / Bai, X.H. / Ren, Y.M. / Thompson, J. / Zhou, C.Z. / Chen, Y.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
B: 6-phospho-beta-glucosidase
E: 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3294
Polymers112,4522
Non-polymers8772
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-11 kcal/mol
Surface area33510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.030, 66.650, 133.350
Angle α, β, γ (deg.)90.00, 136.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 6-phospho-beta-glucosidase /


Mass: 56225.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: bglA-2, SP_0578 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q97S37, UniProt: A0A0H2UP35*PLUS, 6-phospho-beta-glucosidase
#2: Polysaccharide 6-O-phosphono-alpha-L-idopyranose-(1-4)-4-thio-beta-D-glucopyranose / thio-alpha-cellobiose 6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 438.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: thio-alpha-cellobiose 6-phosphate
DescriptorTypeProgram
[][b-D-Glcp4SH]{[(4+S)][a-L-Idop]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% polyethylene glycol 5000MME, 0.1 M sodium citrate tribasic dehydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 43252 / Num. obs: 42473 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.54 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.411→45.954 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2143 5.05 %
Rwork0.1745 --
obs0.1784 42398 97.79 %
all-43356 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.585 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.9123 Å20 Å2-3.3355 Å2
2--27.9526 Å2-0 Å2
3----5.0403 Å2
Refinement stepCycle: LAST / Resolution: 2.411→45.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7522 0 54 202 7778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077777
X-RAY DIFFRACTIONf_angle_d1.14310556
X-RAY DIFFRACTIONf_dihedral_angle_d15.4422826
X-RAY DIFFRACTIONf_chiral_restr0.0831118
X-RAY DIFFRACTIONf_plane_restr0.0051351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.411-2.49720.30571980.21583771X-RAY DIFFRACTION92
2.4972-2.59720.39052120.22453991X-RAY DIFFRACTION99
2.5972-2.71540.28672040.22154106X-RAY DIFFRACTION99
2.7154-2.85850.29782190.1984027X-RAY DIFFRACTION99
2.8585-3.03760.25931940.19244131X-RAY DIFFRACTION100
3.0376-3.27210.27722130.19424096X-RAY DIFFRACTION100
3.2721-3.60120.27022100.19454106X-RAY DIFFRACTION100
3.6012-4.12210.24442370.16234082X-RAY DIFFRACTION100
4.1221-5.19220.17912470.12784082X-RAY DIFFRACTION99
5.1922-45.9540.23752090.16263863X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 1.3121 Å / Origin y: -1.3964 Å / Origin z: 25.7273 Å
111213212223313233
T0.1484 Å2-0.1001 Å2-0.003 Å2-0.1903 Å2-0.0813 Å2--0.1101 Å2
L0.8729 °20.1208 °2-0.174 °2-0.5854 °20.0099 °2--1.3301 °2
S-0.0582 Å °-0.5095 Å °0.1937 Å °0.0695 Å °-0.0725 Å °0.0833 Å °0.0462 Å °0.082 Å °0.0448 Å °
Refinement TLS groupSelection details: all

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