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- PDB-4b3k: Family 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes -

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Basic information

Entry
Database: PDB / ID: 4b3k
TitleFamily 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE / CARBOHYDRATE-ACTIVE ENZYME
Function / homology
Function and homology information


carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStepper, J. / Dabin, J. / Ekloef, J.M. / Thongpoo, P. / Kongsaeree, P.T. / Taylor, E.J. / Turkenburg, J.P. / Brumer, H. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and Activity of the Streptococcus Pyogenes Family Gh1 6-Phospho Beta-Glycosidase Spy1599
Authors: Stepper, J. / Dabin, J. / Ekloef, J.M. / Thongpoo, P. / Kongsaeree, P.T. / Taylor, E.J. / Turkenburg, J.P. / Brumer, H. / Davies, G.J.
History
DepositionJul 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GLUCOSIDASE
B: BETA-GLUCOSIDASE
C: BETA-GLUCOSIDASE
D: BETA-GLUCOSIDASE
E: BETA-GLUCOSIDASE
F: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)330,2436
Polymers330,2436
Non-polymers00
Water1,20767
1
A: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: BETA-GLUCOSIDASE


Theoretical massNumber of molelcules
Total (without water)55,0411
Polymers55,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.420, 190.200, 106.170
Angle α, β, γ (deg.)90.00, 118.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 463
2112B3 - 463
3112C3 - 463
4112D3 - 463
5112E3 - 463
6112F3 - 463

NCS oper:
IDCodeMatrixVector
1given(0.531, -0.202, 0.823), (-0.196, -0.974, -0.112), (0.825, -0.102, -0.557)-59.26208, -41.83821, 99.78091
2given(0.472, -0.004, -0.882), (0.004, -1, 0.006), (-0.882, -0.006, -0.471)3.34486, -50.10485, 4.29425
3given(-0.472, 0.003, 0.881), (0.197, 0.975, 0.102), (-0.859, 0.222, -0.461)-112.29821, -7.37982, 9.11884
4given(-0.535, 0.203, -0.82), (0.018, 0.973, 0.229), (0.845, 0.108, -0.524)-47.45512, -14.99686, 102.58823
5given(-0.999, 0.003, 0.037), (-0.011, -0.975, -0.22), (0.036, -0.22, 0.975)-108.51453, -34.77547, -3.56043

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Components

#1: Protein
BETA-GLUCOSIDASE / 6-PHOSPHO BETA-GLYCOSIDASE


Mass: 55040.555 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS, SF370 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q99YP9, beta-glucosidase, 6-phospho-beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 0.1 M BIS TRIS PROPANE PH7.5, 20% PEG 3350, 0.2M NAF

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorDate: Sep 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.677
11L, -K, H20.323
ReflectionResolution: 2.6→66.56 Å / Num. obs: 105767 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD0

1od0


Resolution: 2.6→66.56 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.842 / SU B: 13.347 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.916 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28577 5282 5 %RANDOM
Rwork0.22278 ---
obs0.22594 100485 93.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.42 Å2
2--0.56 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.6→66.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22602 0 0 67 22669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223346
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.92531824
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92152760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52523.7251224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98153552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.04715132
X-RAY DIFFRACTIONr_chiral_restr0.110.23228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3638medium positional0.040.5
2B3638medium positional0.030.5
3C3638medium positional0.030.5
4D3638medium positional0.030.5
5E3638medium positional0.030.5
6F3638medium positional0.030.5
1A2702tight thermal9.190.5
2B2702tight thermal9.890.5
3C2702tight thermal7.50.5
4D2702tight thermal7.660.5
5E2702tight thermal11.210.5
6F2702tight thermal14.680.5
1A3638medium thermal10.292
2B3638medium thermal112
3C3638medium thermal8.942
4D3638medium thermal9.052
5E3638medium thermal12.772
6F3638medium thermal15.652
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 328 -
Rwork0.333 6475 -
obs--81.83 %

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