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- PDB-1dp0: E. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM -

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Basic information

Entry
Database: PDB / ID: 1dp0
TitleE. COLI BETA-GALACTOSIDASE AT 1.7 ANGSTROM
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMEN / Resolution: 1.7 Å
AuthorsJuers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2000
Title: High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation.
Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1999
Title: Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases
Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
#2: Journal: Nature / Year: 1994
Title: Three-dimensional structure of beta-galactosidase from E. coli
Authors: Juers, D.H. / Huber, R.E. / Matthews, B.W.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of beta-galactosidase from Escherichia coli
Authors: Jacobson, R.H. / Zhang, X.J. / DuBose, R.F. / Matthews, B.W.
History
DepositionDec 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
D: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,625152
Polymers466,0254
Non-polymers9,600148
Water79,6984424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43450 Å2
ΔGint-125 kcal/mol
Surface area135610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.600, 168.380, 200.690
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: 116506.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET 15B (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 112 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4424 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % PEG 8000 100 MM BIS-TRIS 200 MM MGCL(2) 100 MM NACL 10 MM DTT, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1droppure tetramer
210 %PEG80001reservoir
3100 mMBis-Tris1reservoir
4200 mM1reservoirMgCl2
5100 mM1reservoirNaCl
610 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 542319 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.9 / % possible all: 90.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Redundancy: 4.2 % / Num. measured all: 2201152 / Rmerge(I) obs: 0.06 / Biso Wilson estimate: 14.9 Å2
Reflection shell
*PLUS
% possible obs: 97 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMEN / Resolution: 1.7→15 Å / Isotropic thermal model: NONE USED / Stereochemistry target values: TNT
Details: USED CONJUGATE DIRECTION MINIMIZATION OF A LEAST SQUARES RESIDUAL FUNCTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 7905 1.5 %RANDOM
Rwork0.157 ---
all0.158 542319 --
obs0.158 542319 98.6 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE / Bsol: 129 Å2 / ksol: 0.66 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32500 0 484 4424 37408
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.018338041.3
X-RAY DIFFRACTIONt_angle_deg2.916457841.7
X-RAY DIFFRACTIONt_dihedral_angle_d17.3192880
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle14.92481
X-RAY DIFFRACTIONt_trig_c_planes0.0199161.7
X-RAY DIFFRACTIONt_gen_planes0.0248727
X-RAY DIFFRACTIONt_it7.5334680
X-RAY DIFFRACTIONt_nbd0.0953025
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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