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- PDB-1f4a: E. COLI (LACZ) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-ORTHOR... -

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Basic information

Entry
Database: PDB / ID: 1f4a
TitleE. COLI (LACZ) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-ORTHORHOMBIC)
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / alpha/beta barrel / jelly roll barrel / fibronectin / 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 / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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. / Huber, R.E. / Matthews, B.W.
#2: Journal: Nature / Year: 1994
Title: Three-dimensional structure of beta-galactosidase from E. coli
Authors: Jacobson, R.H. / Zhang, X.J. / DuBose, R.F. / Matthews, B.W.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of beta-galactosidase from Escherichia coli
Authors: Jacobson, R.H. / Matthews, B.W.
History
DepositionJun 7, 2000Deposition 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 1.3Nov 29, 2017Group: Advisory / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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)465,15012
Polymers464,9564
Non-polymers1948
Water26,3741464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-95 kcal/mol
Surface area136160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.400, 173.400, 204.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer, which can be generated with the ncs transformations.

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Components

#1: Protein
BETA-GALACTOSIDASE


Mass: 116238.984 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: THE ENDOGENOUS BETA-GALACTOSIDASE WAS PURIFIED FROM E. COLI STRAIN BL21
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1464 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 2KMME, 100 mM Bis-Tris, 200 mM MgCl(2), 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 %PEG80001reservoir
3100 mMBis-Tris1reservoir
4200 mM1reservoirMgCl2
5100 mM1reservoirNaCl
610 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 116158 / Num. obs: 116158 / % possible obs: 88 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.096
Reflection shellHighest resolution: 2.8 Å / Rmerge(I) obs: 0.32 / % possible all: 71
Reflection
*PLUS
% possible obs: 88.3 % / Num. measured all: 299596
Reflection shell
*PLUS
% possible obs: 71 % / Rmerge(I) obs: 0.321

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
MRCHKmodel building
TNT5Erefinement
MRCHKphasing
RefinementResolution: 2.8→25 Å / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1614 -Random, with no special precautions due to the ncs.
Rwork0.167 ---
all-116150 --
obs-116150 88 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE / Bsol: 356 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32952 0 8 1464 34424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.6

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