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- PDB-5ldr: Crystal structure of a cold-adapted dimeric beta-D-galactosidase ... -

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Basic information

Entry
Database: PDB / ID: 5ldr
TitleCrystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose
Components(Beta-D-galactosidase) x 2
KeywordsHYDROLASE / beta-D-galactosidase / cold-adapted / dimeric / complex / galactose
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / : / 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 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / : / 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 / 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 / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / beta-D-galactopyranose / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Beta-D-galactosidase
Similarity search - Component
Biological speciesParacoccus sp. 32d (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsRutkiewicz-Krotewicz, M. / Bujacz, A. / Pietrzyk, A.J. / Sekula, B. / Bujacz, G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d.
Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Sekula, B. / Cieslinski, H. / Wierzbicka-Wos, A. / Kur, J. / Bujacz, A.
History
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-D-galactosidase
B: Beta-D-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,13416
Polymers163,8032
Non-polymers1,33114
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-27 kcal/mol
Surface area51030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.260, 107.580, 201.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-D-galactosidase


Mass: 81958.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D1LZK0, beta-galactosidase
#2: Protein Beta-D-galactosidase


Mass: 81844.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D1LZK0

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Sugars , 2 types, 3 molecules

#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 125 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 24% PEG 2000 0.2M ammonium acetate 0.1M Bis-Tris pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.017 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2013 / Details: mirrors
RadiationMonochromator: 111SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.017 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 29579 / % possible obs: 96.7 % / Redundancy: 3.65 % / CC1/2: 0.983 / Rmerge(I) obs: 0.176 / Net I/σ(I): 7.77
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.63 / CC1/2: 0.643 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EUV

5euv


Resolution: 3.15→46.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.881 / SU B: 29.9 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26658 1480 5 %RANDOM
Rwork0.18394 ---
obs0.18806 28097 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.444 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å2-0 Å20 Å2
2--6.47 Å2-0 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 3.15→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11527 0 83 114 11724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911909
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211113
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.94816246
X-RAY DIFFRACTIONr_angle_other_deg1.172325481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.22651460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19223.116584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29151818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.72615116
X-RAY DIFFRACTIONr_chiral_restr0.10.21779
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113570
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1776.0945848
X-RAY DIFFRACTIONr_mcbond_other5.1746.0935845
X-RAY DIFFRACTIONr_mcangle_it8.2159.1227304
X-RAY DIFFRACTIONr_mcangle_other8.2159.1237305
X-RAY DIFFRACTIONr_scbond_it4.9626.4626061
X-RAY DIFFRACTIONr_scbond_other4.9626.4626062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9969.5598943
X-RAY DIFFRACTIONr_long_range_B_refined12.34648.55313295
X-RAY DIFFRACTIONr_long_range_B_other12.34648.55313295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 104 -
Rwork0.308 1965 -
obs--93.37 %

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