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- PDB-6se8: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB muta... -

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Basic information

Entry
Database: PDB / ID: 6se8
TitleCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E441Q
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric
Function / homology
Function and homology information


lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding
Similarity search - Function
Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 ...Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / MALONATE ION / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. 32cB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å
AuthorsRutkiewicz, M. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST5/00555 Poland
Citation
Journal: Int J Mol Sci / Year: 2019
Title: Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase fromArthrobactersp. 32cB.
Authors: Rutkiewicz, M. / Bujacz, A. / Wanarska, M. / Wierzbicka-Wos, A. / Cieslinski, H.
#1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structural features of cold-adapted dimeric GH2 beta-D-galactosidase from Arthrobacter sp. 32cB.
Authors: Rutkiewicz, M. / Bujacz, A. / Bujacz, G.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,89133
Polymers109,7631
Non-polymers2,12732
Water14,880826
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78266
Polymers219,5272
Non-polymers4,25564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area18170 Å2
ΔGint-93 kcal/mol
Surface area68460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.859, 136.859, 127.082
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1912-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-galactosidase


Mass: 109763.461 Da / Num. of mol.: 1 / Mutation: E441Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. 32cB (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023UGN9, beta-galactosidase

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Non-polymers , 6 types, 858 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.835→46.563 Å / Num. obs: 118383 / % possible obs: 98.8 % / Redundancy: 7.745 % / Biso Wilson estimate: 30.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.086 / Χ2: 1.085 / Net I/σ(I): 13.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.956.3270.5942.1211250219220177800.890.64592.5
1.95-2.088.2470.3694.514877118046180390.970.394100
2.08-2.257.8340.2287.4313197316854168470.9860.244100
2.25-2.468.2910.15711.0812868315529155200.9910.16899.9
2.46-2.757.8550.11215.2411062814089140840.9940.119100
2.75-3.178.2270.08122.8410266112481124780.9960.086100
3.17-3.887.7520.06429.358203710589105830.9970.06899.9
3.88-5.477.6590.0632.4163574830383010.9970.064100
5.47-46.5637.5790.05932.5936010477047510.9960.06399.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETZ

6etz


Resolution: 1.835→46.563 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.65
RfactorNum. reflection% reflection
Rfree0.1647 2101 1.78 %
Rwork0.1345 --
obs0.135 118348 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.26 Å2 / Biso mean: 39.7351 Å2 / Biso min: 19.65 Å2
Refinement stepCycle: final / Resolution: 1.835→46.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 140 826 8648
Biso mean--70.2 44.26 -
Num. residues----1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088124
X-RAY DIFFRACTIONf_angle_d0.96411072
X-RAY DIFFRACTIONf_chiral_restr0.0621165
X-RAY DIFFRACTIONf_plane_restr0.0071506
X-RAY DIFFRACTIONf_dihedral_angle_d16.7524765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8355-1.87810.24061190.2284654284
1.8781-1.92510.20021380.1843762898
1.9251-1.97720.20521390.15857747100
1.9772-2.03530.17281400.1417748100
2.0353-2.1010.18211420.13167825100
2.101-2.17610.16651410.12337790100
2.1761-2.26330.14771400.11697788100
2.2633-2.36630.15911420.12187833100
2.3663-2.4910.15911410.13287825100
2.491-2.64710.20351410.14387794100
2.6471-2.85140.18451420.15297854100
2.8514-3.13830.15271420.14957858100
3.1383-3.59230.14761430.12247913100
3.5923-4.52530.12461430.10357927100
4.5253-46.5630.18891480.15028175100
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)
10.9971-0.0680.30630.3687-0.22141.17020.019-0.1969-0.19240.06920.14190.18730.0169-0.45020.00330.318-0.01020.03410.44480.11660.404518.224830.062938.4977
20.6763-0.09580.01770.3439-0.06520.77460.0142-0.0889-0.08940.0440.0420.04670.0312-0.0568-00.26720.0159-0.00010.23710.02980.267442.54633.0533.6972
30.9461-0.29570.06670.7396-0.13270.63220.10230.1366-0.0651-0.1369-0.0696-0.00020.11360.062100.37410.0451-0.01790.2665-0.00850.298458.132419.400911.4531
40.3258-0.23380.23730.2935-0.08490.24750.21380.2529-0.1883-0.2009-0.13250.06480.19570.2775-0.00490.49340.1529-0.05740.4088-0.07140.373652.482313.9218-10.6237
51.0594-0.0666-0.03250.6014-0.72480.87760.19570.0413-0.0525-0.042-0.03920.0524-0.1607-0.0412-0.00010.33420.0421-0.04410.3328-0.02020.321536.232130.6817-9.5285
60.7498-0.23380.35530.5631-0.36931.30470.15160.1688-0.1813-0.0811-0.09590.03590.29230.15150.00170.34990.0692-0.05050.3282-0.06040.335743.304723.2731-11.4555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 154 )A11 - 154
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 567 )A155 - 567
3X-RAY DIFFRACTION3chain 'A' and (resid 568 through 690 )A568 - 690
4X-RAY DIFFRACTION4chain 'A' and (resid 691 through 739 )A691 - 739
5X-RAY DIFFRACTION5chain 'A' and (resid 740 through 789 )A740 - 789
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 1010 )A790 - 1010

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