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- PDB-4uzs: Crystal structure of Bifidobacterium bifidum beta-galactosidase -

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Basic information

Entry
Database: PDB / ID: 4uzs
TitleCrystal structure of Bifidobacterium bifidum beta-galactosidase
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / LACTASE / FAMILY 42
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / 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 / N-PROPANOL / Beta-galactosidase
Similarity search - Component
Biological speciesBIFIDOBACTERIUM BIFIDUM S17 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.74 Å
AuthorsGodoy, A.S. / Murakami, M.T. / Camilo, C.M. / Bernardes, A. / Polikarpov, I.
CitationJournal: FEBS J. / Year: 2016
Title: Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpah-Galactose.
Authors: Godoy, A.S. / Camilo, C.M. / Kadowaki, M.A. / Muniz, H.D.S. / Santo, M.E. / Murakami, M.T. / Nascimento, A.S. / Polikarpov, I.
History
DepositionSep 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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)233,45920
Polymers231,8353
Non-polymers1,62417
Water48,5682696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20120 Å2
ΔGint-55.1 kcal/mol
Surface area61110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.701, 99.241, 110.757
Angle α, β, γ (deg.)90.00, 106.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 77278.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIFIDOBACTERIUM BIFIDUM S17 (bacteria)
Description: COURTESY OF PROF. CHRISTIAN RIEDEL, ULM UNIVERSITY, GERMANY
Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E3EPA1, beta-galactosidase

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Non-polymers , 5 types, 2713 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2696 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: CRYSTALS DERIVATED WITH HG
Crystal growTemperature: 292 K / pH: 6
Details: 20% (W/V) POLYETHYLENE GLYCOL 3, 350, 0.2 M DIBASIC AMMONIUM TARTRATE AND 4% (W/V) 1-PROPANOL AT 292 K, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2010 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→35.7 Å / Num. obs: 200160 / % possible obs: 98.5 % / Observed criterion σ(I): 1.8 / Redundancy: 3.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.74→35.772 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 10060 5 %
Rwork0.1535 --
obs0.1555 200078 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→35.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16090 0 101 2696 18887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916818
X-RAY DIFFRACTIONf_angle_d1.16522914
X-RAY DIFFRACTIONf_dihedral_angle_d12.8956014
X-RAY DIFFRACTIONf_chiral_restr0.0852390
X-RAY DIFFRACTIONf_plane_restr0.0062998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.75980.37742160.31934566X-RAY DIFFRACTION71
1.7598-1.78050.29813170.25936350X-RAY DIFFRACTION99
1.7805-1.80220.2843130.24256440X-RAY DIFFRACTION100
1.8022-1.8250.28423460.22516328X-RAY DIFFRACTION100
1.825-1.8490.27823480.22026426X-RAY DIFFRACTION100
1.849-1.87440.26543300.21046444X-RAY DIFFRACTION100
1.8744-1.90110.25873010.20356408X-RAY DIFFRACTION100
1.9011-1.92950.22923090.19636376X-RAY DIFFRACTION100
1.9295-1.95970.24783560.19256417X-RAY DIFFRACTION100
1.9597-1.99180.22993490.196397X-RAY DIFFRACTION100
1.9918-2.02610.24333550.18356343X-RAY DIFFRACTION100
2.0261-2.0630.2223600.18756405X-RAY DIFFRACTION100
2.063-2.10260.2313390.17546334X-RAY DIFFRACTION99
2.1026-2.14550.23413290.17516444X-RAY DIFFRACTION100
2.1455-2.19220.21613300.16296353X-RAY DIFFRACTION99
2.1922-2.24320.20783540.15666352X-RAY DIFFRACTION99
2.2432-2.29930.20943360.166434X-RAY DIFFRACTION99
2.2993-2.36140.21183360.15766370X-RAY DIFFRACTION99
2.3614-2.43090.21093510.15696330X-RAY DIFFRACTION99
2.4309-2.50930.21173420.15556382X-RAY DIFFRACTION99
2.5093-2.5990.17883610.15176375X-RAY DIFFRACTION99
2.599-2.7030.22123460.14656371X-RAY DIFFRACTION99
2.703-2.8260.17143390.14386356X-RAY DIFFRACTION99
2.826-2.97490.17813590.13886337X-RAY DIFFRACTION99
2.9749-3.16120.17513140.13486434X-RAY DIFFRACTION99
3.1612-3.40510.15783730.13426358X-RAY DIFFRACTION99
3.4051-3.74750.16123180.12626447X-RAY DIFFRACTION99
3.7475-4.28890.12983280.11346462X-RAY DIFFRACTION99
4.2889-5.40060.14043600.1126426X-RAY DIFFRACTION99
5.4006-35.780.15953450.13776553X-RAY DIFFRACTION99

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