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- PDB-1yq2: beta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1) -

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Basic information

Entry
Database: PDB / ID: 1yq2
Titlebeta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1)
Componentsbeta-galactosidase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 2 / TIM BARREL / HEXAMER
Function / homology
Function and homology information


lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / metal ion 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. ...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. / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Distorted Sandwich / 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
DI(HYDROXYETHYL)ETHER / beta-galactosidase
Similarity search - Component
Biological speciesArthrobacter sp. C2-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSkalova, T. / Dohnalek, J. / Spiwok, V. / Lipovova, P. / Vondrackova, E. / Petrokova, H. / Strnad, H. / Kralova, B. / Hasek, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Cold-active beta-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660kDa Hexamers: Crystal Structure at 1.9A Resolution
Authors: Skalova, T. / Dohnalek, J. / Spiwok, V. / Lipovova, P. / Vondrackova, E. / Petrokova, H. / Duskova, J. / Strnad, H. / Kralova, B. / Hasek, J.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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
C: beta-galactosidase
D: beta-galactosidase
E: beta-galactosidase
F: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)669,20347
Polymers666,8756
Non-polymers2,32841
Water116,5756471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29610 Å2
ΔGint-471 kcal/mol
Surface area200250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.091, 205.698, 140.458
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsHEXAMER IN ASYMMETRIC UNIT IS BIOLOGICAL ASSEMBLY

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
beta-galactosidase / E.C.3.2.1.23


Mass: 111145.906 Da / Num. of mol.: 6 / Mutation: V903M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. C2-2 (bacteria) / Gene: LacZ / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8KRF6, beta-galactosidase

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Non-polymers , 6 types, 6512 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6471 / 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: 2.62 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium chloride, amonium sulphate, sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2003
RadiationMonochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 607777 / Num. obs: 577572 / % possible obs: 95 % / Observed criterion σ(I): -5 / Redundancy: 2.6 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.085 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 24388 / Rsym value: 0.451 / % possible all: 81

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DP0

1dp0


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.96 / SU B: 2.021 / SU ML: 0.06 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / Stereochemistry target values: REFMAC5 DICTIONARY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5775 1 %RANDOM
Rwork0.15701 ---
all0.15702 607830 --
obs0.15702 577466 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.018 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.35 Å2
2--0.64 Å20 Å2
3----0.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47305 0 79 6513 53897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02148787
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.94366761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29856127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66322.5392288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.463156956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.56515497
X-RAY DIFFRACTIONr_chiral_restr0.1050.27091
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0238811
X-RAY DIFFRACTIONr_nbd_refined0.1930.221786
X-RAY DIFFRACTIONr_nbtor_refined0.3070.232454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.25501
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.244
X-RAY DIFFRACTIONr_mcbond_it0.781.530601
X-RAY DIFFRACTIONr_mcangle_it1.399249134
X-RAY DIFFRACTIONr_scbond_it2.206319382
X-RAY DIFFRACTIONr_scangle_it3.5144.517627
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 337 -
Rwork0.218 38384 -
obs-38047 85.52 %

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