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- PDB-4uni: beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lac... -

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Basic information

Entry
Database: PDB / ID: 4uni
Titlebeta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / GH42
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
beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Similarity search - Component
Biological speciesBIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsViborg, A.H. / Fredslund, F. / Katayama, T. / Nielsen, S.K. / Svensson, B. / Kitaoka, M. / Lo Leggio, L. / Abou Hachem, M.
CitationJournal: Mol. Microbiol. / Year: 2014
Title: A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium.
Authors: Viborg, A.H. / Fredslund, F. / Katayama, T. / Nielsen, S.K. / Svensson, B. / Kitaoka, M. / Lo Leggio, L. / Abou Hachem, M.
History
DepositionMay 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 3.0Feb 27, 2019Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_database_proc
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 3.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.2Jan 10, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,22120
Polymers234,9853
Non-polymers2,23617
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-52 kcal/mol
Surface area62150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.520, 199.440, 217.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein BETA-GALACTOSIDASE / / BETA-GAL / BLGAL42A


Mass: 78328.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria)
Strain: BL-04 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: C6A6W5, beta-galactosidase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 361 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62.36 % / Description: NONE
Crystal growpH: 6.5 / Details: 27% PEG1500, 0.01 M MGCL2, 0.1 M MMT BUFFER PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04094
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Sep 28, 2011 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04094 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 92722 / % possible obs: 99.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.07
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KWG

1kwg


Resolution: 2.6→29.727 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 2000 2.2 %
Rwork0.1753 --
obs0.1766 92718 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→29.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16406 0 145 347 16898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517000
X-RAY DIFFRACTIONf_angle_d1.61423140
X-RAY DIFFRACTIONf_dihedral_angle_d16.4556082
X-RAY DIFFRACTIONf_chiral_restr0.0892460
X-RAY DIFFRACTIONf_plane_restr0.0093037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6650.35431350.28966093X-RAY DIFFRACTION95
2.665-2.7370.34941410.26556438X-RAY DIFFRACTION100
2.737-2.81740.31581420.24886450X-RAY DIFFRACTION100
2.8174-2.90830.35121420.24466448X-RAY DIFFRACTION100
2.9083-3.01210.35021430.23686461X-RAY DIFFRACTION100
3.0121-3.13260.31851430.22776454X-RAY DIFFRACTION100
3.1326-3.2750.27151430.21236483X-RAY DIFFRACTION100
3.275-3.44750.23731420.1966468X-RAY DIFFRACTION100
3.4475-3.66310.25171430.18626490X-RAY DIFFRACTION100
3.6631-3.94530.24111430.16966508X-RAY DIFFRACTION100
3.9453-4.34130.20391450.14586517X-RAY DIFFRACTION100
4.3413-4.96690.18031430.12826543X-RAY DIFFRACTION100
4.9669-6.24820.1841450.13826605X-RAY DIFFRACTION100
6.2482-29.72860.1611500.13426760X-RAY DIFFRACTION100

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