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- PDB-3oba: Structure of the beta-galactosidase from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 3oba
TitleStructure of the beta-galactosidase from Kluyveromyces lactis
ComponentsBeta-galactosidase
KeywordsHYDROLASE / TIM Barrel / Tetramer / GH2 / Glycosidase
Function / homology
Function and homology information


: / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
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; Chain A, domain 5 - #10 ...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 / 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 / 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
MANGANESE (III) ION / Beta-galactosidase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsFernandez-Leiro, R. / Pereira-Rodriguez, A. / Becerra, M. / Gonzalez-Siso, I. / Cerdan, M.E. / Sanz-Aparicio, J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural basis of specificity in tetrameric Kluyveromyces lactis beta-galactosidase.
Authors: Pereira-Rodriguez, A. / Fernandez-Leiro, R. / Gonzalez-Siso, M.I. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: 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 / struct_ncs_dom_lim / 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_label_asym_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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,69018
Polymers474,5494
Non-polymers1,14114
Water30,0131666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19680 Å2
ΔGint-68 kcal/mol
Surface area141600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.030, 153.340, 216.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 1025 / Label seq-ID: 9 - 1032

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB
3DC
4BD

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Components

#1: Protein
Beta-galactosidase / Beta-gal / Lactase


Mass: 118637.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: Y1140 / Gene: KLLA0B14883g, LAC4 / Plasmid: YEPFLAG-1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ3505 / References: UniProt: P00723, beta-galactosidase
#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1666 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24 % Polyethylen Glycol (PEG) 3350, 0.1 M BisTris pH 7.5, 0.2 M Sodium Tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→125.067 Å / Num. all: 121272 / Num. obs: 121272 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.172 / Rsym value: 0.172 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.75-2.97.10.5361.4123972174990.536100
2.9-3.077.30.3862120391165900.386100
3.07-3.297.40.272.8115002156320.27100
3.29-3.557.40.1894107430145700.189100
3.55-3.897.40.1395.499032134620.139100
3.89-4.357.30.1116.689156121930.111100
4.35-5.027.20.0967.378012108040.096100
5.02-6.1570.1245.76424892070.124100
6.15-8.76.70.1016.94840071870.10199.9
8.7-62.53470.05312.22897141280.05399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YQ2

1yq2


Resolution: 2.75→62.57 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.1881 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8572 / SU B: 12.922 / SU ML: 0.26 / SU Rfree: 0.3762 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 6092 5 %RANDOM
Rwork0.2067 ---
obs0.2085 121060 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.91 Å2 / Biso mean: 19.5681 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.75→62.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33300 0 64 1666 35030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02234294
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.94146506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35654092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90724.6851776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.286155688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.40815136
X-RAY DIFFRACTIONr_chiral_restr0.0810.24832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126716
X-RAY DIFFRACTIONr_mcbond_it0.4121.520404
X-RAY DIFFRACTIONr_mcangle_it0.816233040
X-RAY DIFFRACTIONr_scbond_it1.024313890
X-RAY DIFFRACTIONr_scangle_it1.8624.513466
Refine LS restraints NCS

Ens-ID: 1 / Number: 8325 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.030.05
2CTIGHT POSITIONAL0.030.05
3DTIGHT POSITIONAL0.030.05
4BTIGHT POSITIONAL0.030.05
1ATIGHT THERMAL0.040.5
2CTIGHT THERMAL0.040.5
3DTIGHT THERMAL0.040.5
4BTIGHT THERMAL0.040.5
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 450 -
Rwork0.296 8390 -
all-8840 -
obs--99.82 %

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