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- PDB-3pn8: The crystal structure of 6-phospho-beta-glucosidase from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 3pn8
TitleThe crystal structure of 6-phospho-beta-glucosidase from Streptococcus mutans UA159
ComponentsPutative phospho-beta-glucosidase
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / (beta/alpha)8 barrel / Beta-Glucosidase / cytoplasmic
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase 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
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Phospho-beta-glucosidase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.693 Å
AuthorsTan, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of 6-phospho-beta-glucosidase from Streptococcus mutants UA159
Authors: Tan, K. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Other
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,05234
Polymers112,3582
Non-polymers2,69432
Water10,178565
1
A: Putative phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81021
Polymers56,1791
Non-polymers1,63120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,24213
Polymers56,1791
Non-polymers1,06312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-124 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.890, 91.038, 98.563
Angle α, β, γ (deg.)90.00, 98.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

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Components

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


Mass: 56178.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: bgl, SMU_1601, Streptococcus mutans / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DT00, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium Sulfate, 0.1M Tris:HCl, 40% (w/v) PEG 400, pH 8.5, 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.7→36 Å / Num. all: 112307 / Num. obs: 112307 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 20.61 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 26.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5460 / % possible all: 97.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.693→35.859 Å / SU ML: 0.17 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 5294 5 %random
Rwork0.163 ---
obs0.1645 105937 92.73 %-
all-105937 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.63 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso min: 21.37 Å2
Baniso -1Baniso -2Baniso -3
1-13.0643 Å20 Å2-2.7456 Å2
2---1.8633 Å20 Å2
3----11.201 Å2
Refinement stepCycle: LAST / Resolution: 1.693→35.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7795 0 164 565 8524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068220
X-RAY DIFFRACTIONf_angle_d0.93911095
X-RAY DIFFRACTIONf_dihedral_angle_d17.9122909
X-RAY DIFFRACTIONf_chiral_restr0.0731097
X-RAY DIFFRACTIONf_plane_restr0.0041430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.693-1.75350.30454150.26088387X-RAY DIFFRACTION78
1.7535-1.82370.2785030.2159193X-RAY DIFFRACTION85
1.8237-1.90670.23585240.18859587X-RAY DIFFRACTION89
1.9067-2.00730.20175470.164610076X-RAY DIFFRACTION93
2.0073-2.1330.20575380.159410386X-RAY DIFFRACTION96
2.133-2.29770.1975330.151610591X-RAY DIFFRACTION98
2.2977-2.52880.18535670.150810758X-RAY DIFFRACTION99
2.5288-2.89460.19135900.163610741X-RAY DIFFRACTION99
2.8946-3.64640.195140.171810754X-RAY DIFFRACTION98
3.6464-35.86650.16415630.141610170X-RAY DIFFRACTION92
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)
10.63750.1466-0.06272.0819-0.86510.8376-0.09410.1077-0.0555-0.57410.0094-0.33660.2397-0.0210.08650.2332-0.01170.09270.105-0.01920.161913.4495-0.812733.1406
20.5135-0.26870.25481.5298-0.41551.2296-0.104-0.1669-0.04060.46080.23650.1143-0.1533-0.2745-0.12470.27990.12030.04770.24590.05510.1712-4.397-0.556374.3428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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