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- PDB-4mad: Crystal structure of beta-galactosidase C (BgaC) from Bacillus ci... -

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Basic information

Entry
Database: PDB / ID: 4mad
TitleCrystal structure of beta-galactosidase C (BgaC) from Bacillus circulans ATCC 31382
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Beta-Galactosidase / bgaC / GH-A / (b/a)8/GH / family 35
Function / homology
Function and homology information


vacuole / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 ...Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKamerke, C. / You, D.J. / Kanaya, S. / Elling, L.
CitationJournal: J.Biotechnol. / Year: 2014
Title: Rational design of a glycosynthase by the crystal structure of beta-galactosidase from Bacillus circulans (BgaC) and its use for the synthesis of N-acetyllactosamine type 1 glycan structures.
Authors: Henze, M. / You, D.J. / Kamerke, C. / Hoffmann, N. / Angkawidjaja, C. / Ernst, S. / Pietruszka, J. / Kanaya, S. / Elling, L.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5195
Polymers137,1582
Non-polymers3603
Water7,656425
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8203
Polymers68,5791
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6992
Polymers68,5791
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.268, 93.122, 119.567
Angle α, β, γ (deg.)90.000, 125.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-galactosidase


Mass: 68579.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: ATCC 31382 / Gene: bgaC, D88750 / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31341, hyaluronoglucosaminidase
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.36 Å3/Da / Density % sol: 47.93 % / Mosaicity: 0.805 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mg/ml Protein in 10mM Tris-HCl and 1mM EDTA (pH 7.5), Reservoir (20% (w/v) PEG 6000, 100mM HEPES, 0.2M NaCl, pH 7.0), Protein:Reservoir=1:1 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Apr 9, 2012
RadiationMonochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 117585 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Χ2: 0.963 / Net I/σ(I): 24.672
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8310.40.5258880.467199.5
1.83-1.8610.40.45558400.476199.5
1.86-1.910.40.38658520.513199.5
1.9-1.9410.40.33958620.534199.6
1.94-1.9810.50.29858440.559199.6
1.98-2.0310.50.25658730.601199.7
2.03-2.0810.50.2358490.621199.8
2.08-2.1310.60.20558670.654199.7
2.13-2.210.60.18558840.689199.8
2.2-2.2710.60.16658710.723199.9
2.27-2.3510.50.15158800.746199.8
2.35-2.4410.50.1459200.784199.9
2.44-2.5510.50.12758390.83199.9
2.55-2.6910.50.11859060.936199.8
2.69-2.8610.50.11559031.146199.9
2.86-3.0810.50.11458971.568199.8
3.08-3.3910.40.10358941.913199.6
3.39-3.8810.30.08558951.893199.1
3.88-4.8810.10.0758351.869198.2
4.88-5010.40.06659861.769199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å41.66 Å
Translation1.96 Å41.66 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3A

3d3a


Resolution: 1.8→41.66 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.488 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 5891 5 %RANDOM
Rwork0.1811 ---
all0.183 ---
obs0.1829 117416 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.35 Å2 / Biso mean: 22.489 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-1.93 Å2
2---0.71 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9435 0 24 425 9884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229725
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.95213194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.67751165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44824.303488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.063151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1281544
X-RAY DIFFRACTIONr_chiral_restr0.1030.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0217558
X-RAY DIFFRACTIONr_mcbond_it1.8051.55793
X-RAY DIFFRACTIONr_mcangle_it2.79829364
X-RAY DIFFRACTIONr_scbond_it4.20133932
X-RAY DIFFRACTIONr_scangle_it6.2854.53830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.2664190.2218220872299.048
1.847-1.8970.2654330.1997998848199.41
1.897-1.9520.2314160.1867753821399.464
1.952-2.0120.2284110.1887546799299.562
2.012-2.0780.2483650.1887405779399.705
2.078-2.1510.213550.1827125750799.64
2.151-2.2320.2433450.1876884725299.683
2.232-2.3240.2353440.1836628698799.785
2.324-2.4270.2313260.186365670399.821
2.427-2.5450.2443370.1886045639399.828
2.545-2.6830.2353090.1965753608899.573
2.683-2.8450.2563020.2085492580999.742
2.845-3.0420.2312810.2045116541499.686
3.042-3.2850.2272580.2014800508099.567
3.285-3.5980.2022320.1784376464399.246
3.598-4.0220.1752080.163963421898.886
4.022-4.6430.1572050.1413444373197.802
4.643-5.6830.1931610.1483007318899.373
5.683-8.0240.1811200.1732321244699.796
8.024-97.1350.17640.1771284140595.943

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