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- PDB-3e1f: E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose -

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Basic information

Entry
Database: PDB / ID: 3e1f
TitleE.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose
ComponentsBeta-galactosidase
KeywordsHYDROLASE / His-418-Glu BETA-GALACTOSIDASE HYDROLASE TIM BARREL (ALPHA/BETA BARREL) JELLY-ROLL BARREL IMMUNOGLOBULIN BETA SUPERSANDWICH / Glycosidase
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / 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 ...Glycoside hydrolase, family 2, beta-galactosidase / 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 / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuber, R.E. / Dugdale, M.L.
CitationJournal: Protein Sci. / Year: 2009
Title: Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).
Authors: Juers, D.H. / Rob, B. / Dugdale, M.L. / Rahimzadeh, N. / Giang, C. / Lee, M. / Matthews, B.W. / Huber, R.E.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 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
1: Beta-galactosidase
2: Beta-galactosidase
3: Beta-galactosidase
4: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,676108
Polymers465,9894
Non-polymers7,687104
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-31 kcal/mol
Surface area135010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.370, 152.870, 132.120
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 12 molecules 1234

#1: Protein
Beta-galactosidase / Lactase


Mass: 116497.234 Da / Num. of mol.: 4 / Fragment: BETA-GALACTOSIDASE / Mutation: H418E
Source method: isolated from a genetically manipulated source
Details: N-terminal His tag / Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: lacZ, b0344, JW0335 / Plasmid: pBAD/HIS/LACZ / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P00722, beta-galactosidase
#5: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
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

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Non-polymers , 4 types, 424 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 73 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2007 / Details: KOHZU: Double Crystal Si (111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 3→98.54 Å / Num. all: 90713 / Num. obs: 90713 / Observed criterion σ(F): 0 / Limit h max: 41 / Limit h min: -42 / Limit k max: 50 / Limit k min: -42 / Limit l max: 44 / Limit l min: 0 / Observed criterion F max: 2426618.92 / Observed criterion F min: 43.396
Reflection shellHighest resolution: 3 Å / Num. unique all: 90713

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JYX

1jyx


Resolution: 3→98.54 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 411 Solvent 324 CNS ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 411 Solvent 324 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/water.param CNS_TOPPAR/ion.param ../cns_1/dms_xplor_par.txt ../cns_1/gal_xplor_par.txt CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/water.top CNS_TOPPAR/ion.top ../cns_1/dms_xplor_par.txt ../cns_1/gal_xplor_top.txt
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4529 5 %1.5%, consistent with previous structures.
Rwork0.218 ---
all-99534 --
obs-90712 91.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 25.6967 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 134.93 Å2 / Biso mean: 43.38 Å2 / Biso min: 1.31 Å2
Baniso -1Baniso -2Baniso -3
1-13.08 Å20 Å2-0.54 Å2
2---4.42 Å20 Å2
3----8.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Luzzati d res high-3
Refinement stepCycle: LAST / Resolution: 3→98.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32496 0 411 328 33235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg25.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.93
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3-3.140.3594574.50.32296410.017123721009881.6
3.14-3.30.3224914.60.288101740.015124301066585.8
3.3-3.510.3015615.10.254105090.013123811107089.4
3.51-3.780.25257550.221109300.011124721150592.2
3.78-4.160.2316185.20.201112320.009124171185095.4
4.16-4.760.2116105.10.17112860.009124431189695.6
4.76-60.2266055.10.192112290.009124631183494.9
6-98.540.2276125.20.212111820.009126251179493.4

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