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- PDB-4uoq: Nucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifid... -

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Basic information

Entry
Database: PDB / ID: 4uoq
TitleNucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / :
Similarity search - Component
Biological speciesBIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionJun 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _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: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,92620
Polymers234,8113
Non-polymers2,11617
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18800 Å2
ΔGint-40.3 kcal/mol
Surface area65280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.560, 150.560, 237.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 78270.242 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria)
Strain: BL-04 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: C6A6W5, beta-galactosidase

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Non-polymers , 5 types, 316 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.23 Å3/Da / Density % sol: 62.36 % / Description: NONE
Crystal growpH: 6.5 / Details: 29% PEG1500, 0.01 MM 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: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Sep 10, 2012 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 85508 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 46.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.65
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UNI

4uni


Resolution: 2.7→19.93 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2000 2.3 %
Rwork0.1809 --
obs0.182 85449 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16328 0 137 299 16764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916909
X-RAY DIFFRACTIONf_angle_d1.18922997
X-RAY DIFFRACTIONf_dihedral_angle_d14.9536056
X-RAY DIFFRACTIONf_chiral_restr0.0742436
X-RAY DIFFRACTIONf_plane_restr0.0063015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76730.30971410.24545876X-RAY DIFFRACTION100
2.7673-2.84190.30491420.2345952X-RAY DIFFRACTION100
2.8419-2.92530.2831400.23355878X-RAY DIFFRACTION100
2.9253-3.01940.29351450.2375915X-RAY DIFFRACTION100
3.0194-3.1270.26671450.2385880X-RAY DIFFRACTION100
3.127-3.25160.26331390.2275908X-RAY DIFFRACTION100
3.2516-3.39890.26091370.21325942X-RAY DIFFRACTION100
3.3989-3.57720.25291410.19565935X-RAY DIFFRACTION100
3.5772-3.79980.22641420.1865932X-RAY DIFFRACTION100
3.7998-4.09090.21941450.16775935X-RAY DIFFRACTION99
4.0909-4.49830.20611390.14935959X-RAY DIFFRACTION100
4.4983-5.13940.19481470.14186006X-RAY DIFFRACTION100
5.1394-6.43870.17241480.16036079X-RAY DIFFRACTION100
6.4387-19.9310.18551490.14636252X-RAY DIFFRACTION100

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