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- PDB-3tty: Crystal structure of beta-galactosidase from Bacillus circulans s... -

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Basic information

Entry
Database: PDB / ID: 3tty
TitleCrystal structure of beta-galactosidase from Bacillus circulans sp. alkalophilus in complex with galactose
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Tim Barrel / Glycoside hydrolase
Function / homology
Function and homology information


Class I glutamine amidotransferase (GATase) domain / Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-galactopyranose
Similarity search - Component
Biological speciesBacillus circulans subsp. alkalophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMaksimainen, M. / Hakulinen, N. / Rouvinen, J.
CitationJournal: Febs J. / Year: 2012
Title: Structural analysis, enzymatic characterization, and catalytic mechanisms of beta-galactosidase from Bacillus circulans sp. alkalophilus.
Authors: Maksimainen, M. / Paavilainen, S. / Hakulinen, N. / Rouvinen, J.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,95418
Polymers464,4806
Non-polymers1,47312
Water45,3262516
1
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,9779
Polymers232,2403
Non-polymers7376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-58 kcal/mol
Surface area63660 Å2
MethodPISA
2
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,9779
Polymers232,2403
Non-polymers7376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-58 kcal/mol
Surface area63810 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.200, 228.200, 246.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Beta-galactosidase / / Beta-gal


Mass: 77413.359 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Bacillus circulans subsp. alkalophilus (bacteria)
References: beta-galactosidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2516 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6-9% PEG 3350, 0.1M magnesium sulfate, 0.1M bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 225561 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 22.18 Å2
Reflection shellResolution: 2.25→2.3 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TTS

3tts


Resolution: 2.25→47.57 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 11276 5 %RANDOM
Rwork0.16 ---
all0.164 225561 --
obs0.1625 225527 99.19 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.456 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7875 Å20 Å2-0 Å2
2--1.7875 Å20 Å2
3----3.575 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32676 0 78 2516 35270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733618
X-RAY DIFFRACTIONf_angle_d1.11645588
X-RAY DIFFRACTIONf_dihedral_angle_d15.2512354
X-RAY DIFFRACTIONf_chiral_restr0.0834710
X-RAY DIFFRACTIONf_plane_restr0.0055904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33040.285511130.211921165X-RAY DIFFRACTION98
2.3304-2.42370.272311310.202821472X-RAY DIFFRACTION99
2.4237-2.5340.26711250.19521389X-RAY DIFFRACTION99
2.534-2.66760.259811300.191321471X-RAY DIFFRACTION99
2.6676-2.83470.242811300.179721456X-RAY DIFFRACTION99
2.8347-3.05360.229211310.171721504X-RAY DIFFRACTION99
3.0536-3.36080.221911300.167921466X-RAY DIFFRACTION100
3.3608-3.84690.19411300.151221461X-RAY DIFFRACTION99
3.8469-4.8460.152711260.117721395X-RAY DIFFRACTION99
4.846-47.58060.165111300.133421472X-RAY DIFFRACTION99

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