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- PDB-3dym: E. coli (lacZ) beta-galactosidase (H418E) -

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Basic information

Entry
Database: PDB / ID: 3dym
TitleE. coli (lacZ) beta-galactosidase (H418E)
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / 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 / Glycosyl hydrolases family 2 signature 1. ...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 / 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
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJuers, D.H. / Huber, R.E. / Matthews, B.W.
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
DepositionJul 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_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_comp_id / _pdbx_struct_conn_angle.value / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _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
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _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
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,007112
Polymers465,9894
Non-polymers7,018108
Water62,4043464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16870 Å2
ΔGint-35 kcal/mol
Surface area135220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.340, 167.160, 200.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-galactosidase /


Mass: 116497.234 Da / Num. of mol.: 4 / Mutation: H418E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: lacZ, b0344, JW0335 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00722, beta-galactosidase
#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.: 16 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 82 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3464 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.05→34.5 Å / Num. all: 309949 / Num. obs: 309949 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.4 / Num. unique all: 22484 / Rsym value: 0.316 / % possible all: 98.2

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DP0

1dp0


Resolution: 2.05→34.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4471 1.4 %random
Rwork0.158 ---
all-309949 --
obs-309949 99.4 %-
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å20 Å2
2--6.71 Å20 Å2
3----3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32496 0 354 3464 36314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_dihedral_angle_d17.8

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