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- PDB-4b3l: Family 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes -

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Basic information

Entry
Database: PDB / ID: 4b3l
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: 2.51 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 "BA" 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
Water30617
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)107.830, 198.040, 107.880
Angle α, β, γ (deg.)90.00, 118.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A3 - 463
2113B3 - 463
3113C3 - 463
4113D3 - 463
1126E3 - 463
2126F3 - 463

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.491, -0.04, -0.87), (-0.039, -0.999, 0.024), (-0.87, 0.022, -0.492)50.89301, 50.62036, 85.19722
2given(-0.999, 0.009, 0.031), (-0.014, -0.987, -0.163), (0.029, -0.163, 0.986)9.30869, 49.0272, 4.11664
3given(-0.485, 0.176, -0.857), (0.045, 0.983, 0.177), (0.874, 0.047, -0.485)50.56327, 1.51357, 75.3611
4given(-0.5, 0.037, 0.865), (0.179, 0.982, 0.062), (-0.847, 0.185, -0.498)-37.34318
5given(0.55, -0.186, 0.814), (-0.175, -0.979, -0.106), (0.817, -0.084, -0.571)-37.05718

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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.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK AAK34377.1

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.1 M BIS TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M NAF

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorDate: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.51→99.02 Å / Num. obs: 134562 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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: 2.51→94.75 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.966 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.281 / 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
Rfree0.26139 6762 5 %RANDOM
Rwork0.20486 ---
obs0.20767 127798 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.1 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.51→94.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22602 0 0 17 22619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223346
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215748
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.92531824
X-RAY DIFFRACTIONr_angle_other_deg0.987338014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88252760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39423.7251224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.846153552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.57115132
X-RAY DIFFRACTIONr_chiral_restr0.1110.23228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118546
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025216
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2704tight positional0.040.05
12B2704tight positional0.040.05
13C2704tight positional0.040.05
14D2704tight positional0.040.05
11A3642loose positional0.045
12B3642loose positional0.055
13C3642loose positional0.055
14D3642loose positional0.045
21E6316loose positional0.355
22F6316loose positional0.355
11A2704tight thermal3.940.5
12B2704tight thermal4.110.5
13C2704tight thermal4.420.5
14D2704tight thermal4.220.5
11A3642loose thermal4.6110
12B3642loose thermal5.0510
13C3642loose thermal5.310
14D3642loose thermal5.1810
21E6316loose thermal4.8710
22F6316loose thermal4.8710
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 471 -
Rwork0.337 9457 -
obs--99.95 %

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