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- PDB-5vym: Crystal structure of beta-galactosidase from Bifidobacterium adol... -

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Basic information

Entry
Database: PDB / ID: 5vym
TitleCrystal structure of beta-galactosidase from Bifidobacterium adolescentis
ComponentsBeta-galactosidase BgaB
KeywordsHYDROLASE / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-galactosidase BgaB
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.456 Å
AuthorsChang, C. / Cuff, M. / Tesar, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: Crystal structure of beta-galactosidase from Bifidobacterium adolescentis
Authors: Chang, C. / Cuff, M. / Tesar, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 BgaB
B: Beta-galactosidase BgaB


Theoretical massNumber of molelcules
Total (without water)50,0492
Polymers50,0492
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-38 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.549, 90.549, 278.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Beta-galactosidase BgaB / Beta-gal / Beta-Gal II


Mass: 25024.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (bacteria)
Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / Gene: bgaB, bgaLII, BAD_1401 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A1A399, beta-galactosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Lithiumsulfate, 0.1M Sodium acetate, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.37762 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37762 Å / Relative weight: 1
ReflectionResolution: 2.45→36.11 Å / Num. obs: 36438 / % possible obs: 98.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 38.78 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.027 / Rrim(I) all: 0.081 / Χ2: 0.901 / Net I/σ(I): 8.6 / Num. measured all: 205921
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.4990.78612280.8560.2640.8320.845100
2.49-2.5490.71812440.8830.2430.7610.852100
2.54-2.598.90.6212430.9050.2110.6580.849100
2.59-2.648.90.53212410.9180.180.5640.89299.9
2.64-2.78.80.4312510.9420.1460.4560.903100
2.7-2.768.80.35712450.9730.1220.3790.888100
2.76-2.838.60.32812760.9630.1120.3480.92100
2.83-2.98.60.26612480.970.0910.2830.98199.8
2.9-2.998.50.23612460.9740.0810.2510.951100
2.99-3.098.40.18912470.9930.0650.2010.99399.8
3.09-3.28.20.12912650.9890.0440.1370.9499.5
3.2-3.328.10.0912680.9930.0310.0960.94599.5
3.32-3.4880.07412670.9940.0260.0790.92199.2
3.48-3.667.90.06212540.9960.0220.0660.93499.1
3.66-3.897.80.04512620.9970.0150.0480.90597.8
3.89-4.197.50.03912620.9970.0130.0420.87397.9
4.19-4.617.40.03312580.9980.0120.0350.82896.3
4.61-5.287.10.03112820.9980.0110.0330.76196.9
5.28-6.656.80.03113070.9980.0110.0330.70796.2
6.65-506.80.03314470.9970.0130.0361.10596.7

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Processing

Software
NameVersionClassification
PHENIXdev_2650refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZS

4uzs


Resolution: 2.456→36.11 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 3000 8.23 %
Rwork0.1815 33438 -
obs0.1852 36438 78.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.79 Å2 / Biso mean: 47.9097 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 2.456→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 0 123 3397
Biso mean---44.64 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023347
X-RAY DIFFRACTIONf_angle_d0.424567
X-RAY DIFFRACTIONf_chiral_restr0.039512
X-RAY DIFFRACTIONf_plane_restr0.003591
X-RAY DIFFRACTIONf_dihedral_angle_d10.6831904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4561-2.49640.3581750.26284592041
2.4964-2.53940.3454840.2749976106049
2.5394-2.58560.3584990.27071159125856
2.5856-2.63530.33381120.25531220133261
2.6353-2.68910.3271170.26171280139763
2.6891-2.74750.29381190.25211333145264
2.7475-2.81140.35481220.2741339146167
2.8114-2.88170.30051410.25591364150569
2.8817-2.95960.28541250.24091443156870
2.9596-3.04660.31071350.25341484161973
3.0466-3.14490.29861440.22341633177780
3.1449-3.25720.27811600.1981778193888
3.2572-3.38760.2451720.19441873204592
3.3876-3.54160.22591680.18951944211296
3.5416-3.72810.20811690.17021989215897
3.7281-3.96150.22291800.15291971215197
3.9615-4.26690.15231780.13341955213396
4.2669-4.69540.17941770.13271952212996
4.6954-5.3730.16891740.14171951212596
5.373-6.76210.22591720.16951944211696
6.7621-36.11340.18661770.17762005218298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38180.0482-0.37690.25940.08370.4196-0.06680.0810.001-0.08690.0662-0.16890.1850.0588-00.2653-0.02950.0150.2203-0.05070.226420.62924.3873-25.2606
20.4713-0.1608-0.29380.42360.20550.2043-0.1185-0.1054-0.08910.13320.14720.00850.1457-0.00220.00480.1214-0.01180.00160.09620.0110.073614.462228.9492-10.2628
30.36150.07130.1320.2359-0.18850.23250.0699-0.13990.3649-0.03230.0926-0.3128-0.32710.49670.00070.3361-0.13710.08090.464-0.16130.470912.675854.45284.2774
40.39910.1643-0.07180.2416-0.06830.2680.1268-0.02150.16460.06810.0796-0.0254-0.02890.37290.01060.3261-0.06860.08620.2873-0.03710.32984.898252.9421-0.0751
50.8310.2592-0.6480.6793-0.08820.95830.0034-0.07670.02670.15330.03980.0865-0.04860.0899-00.12050.01120.02490.1616-0.00530.1334-2.560741.83924.2851
60.5683-0.3685-0.04660.29330.07570.3708-0.16960.1494-0.23780.1516-0.01250.37640.2174-0.4262-0.08870.3229-0.17450.09210.2321-0.04670.32924.08615.5321-17.9221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 59 )A0 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 140 )A60 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 183 )A141 - 183
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 225 )A184 - 225
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 129 )B0 - 129
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 224 )B130 - 224

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