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- PDB-6quc: Truncated beta-galactosidase III from Bifidobacterium bifidum -

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Basic information

Entry
Database: PDB / ID: 6quc
TitleTruncated beta-galactosidase III from Bifidobacterium bifidum
ComponentsBeta-galactosidase
KeywordsSUGAR BINDING PROTEIN / TIM BARREL / GLYCOSIDE HYDROLASE / HYDROLASE
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain ...Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThirup, S.S. / Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Agency for Science Technology and Innovation Denmark
CitationJournal: To Be Published
Title: Truncated beta-galactosidase III from Bifidobacterium bifidum
Authors: Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M. / Thirup, S.S. / Larsen, M.K. / Cramer, J.F.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)191,29212
Polymers190,7182
Non-polymers57510
Water14,412800
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6466
Polymers95,3591
Non-polymers2875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6466
Polymers95,3591
Non-polymers2875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.500, 119.683, 144.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-galactosidase


Mass: 95358.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q9F4D5, beta-galactosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 550mme 100 mM Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.1 Å / Num. obs: 91305 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9057 / CC1/2: 0.854 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GM8

3gm8


Resolution: 2.3→46.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.95
RfactorNum. reflection% reflection
Rfree0.2176 1980 2.17 %
Rwork0.1878 --
obs0.1884 91044 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13058 0 34 800 13892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313380
X-RAY DIFFRACTIONf_angle_d0.65118200
X-RAY DIFFRACTIONf_dihedral_angle_d10.5647778
X-RAY DIFFRACTIONf_chiral_restr0.0472004
X-RAY DIFFRACTIONf_plane_restr0.0032368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.3461320.29346123X-RAY DIFFRACTION97
2.3575-2.42130.27281420.24726323X-RAY DIFFRACTION100
2.4213-2.49250.30081430.22466364X-RAY DIFFRACTION100
2.4925-2.57290.27521390.22236316X-RAY DIFFRACTION100
2.5729-2.66490.25751380.23666321X-RAY DIFFRACTION100
2.6649-2.77160.31181440.23556340X-RAY DIFFRACTION99
2.7716-2.89770.23221390.21816339X-RAY DIFFRACTION100
2.8977-3.05050.22951410.21336353X-RAY DIFFRACTION100
3.0505-3.24150.22271390.20926362X-RAY DIFFRACTION99
3.2415-3.49170.23321400.20536360X-RAY DIFFRACTION99
3.4917-3.8430.26811420.23086240X-RAY DIFFRACTION97
3.843-4.39870.17061410.15766371X-RAY DIFFRACTION99
4.3987-5.54040.16321460.13086509X-RAY DIFFRACTION100
5.5404-46.10890.15931540.12936743X-RAY DIFFRACTION100
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)
10.5218-0.33740.10990.241-0.17410.2563-0.1567-0.0944-0.20420.470.08390.5110.1225-0.0411-0.00030.6620.00640.13360.3804-0.01750.4263-6.6043-0.0645.2046
20.45390.033-0.10780.2135-0.18860.1626-0.022-0.03810.00440.306-0.0136-0.00160.0497-0.025500.58010.0001-0.00590.3363-0.05350.35122.0610.176641.6846
30.7686-0.3817-0.17441.20640.03850.79270.04450.1507-0.0942-0.0889-0.07110.10070.00240.0623-00.3734-0.0063-0.00690.3496-0.0670.31510.82511.711917.3753
41.0055-0.3259-0.14461.4749-0.30250.8360.07460.12250.1946-0.02140.01240.2945-0.1457-0.174900.42060.0283-0.01080.3465-0.02130.4294-15.378522.492822.9156
50.2877-0.2494-0.30210.22770.16750.59410.10160.10790.3415-0.0632-0.1061-0.16640.00910.0522-00.370.006-0.01160.44980.05430.4626-28.1415-21.9067-8.2202
60.5308-0.16390.02540.4810.10650.28250.0146-0.0256-0.00690.0153-0.0156-0.01320.0307-0.0063-00.2574-0.0131-0.03190.35390.0040.325-25.9593-34.953710.0403
70.8496-0.00530.12580.6979-0.13030.7583-0.032-0.15670.03280.0838-00.0995-0.0464-0.084800.28850.0048-0.01630.382-0.03630.3506-49.6279-27.736613.4618
80.4766-0.3035-0.08660.52360.06560.6587-0.0301-0.31590.35410.2941-0.04780.1607-0.3991-0.1449-0.00010.61540.07410.03220.5864-0.22890.571-57.3736-1.680229.612
90.2426-0.0558-0.12330.41320.04050.55970.0096-0.17590.5392-0.0526-0.033-0.1292-0.24120.093600.4573-0.0232-0.06310.4073-0.07190.6433-36.8523-0.98496.2551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 912 )
5X-RAY DIFFRACTION5chain 'B' and (resid 54 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 346 )
7X-RAY DIFFRACTION7chain 'B' and (resid 347 through 674 )
8X-RAY DIFFRACTION8chain 'B' and (resid 675 through 807 )
9X-RAY DIFFRACTION9chain 'B' and (resid 808 through 912 )

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