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- PDB-4v45: E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME I... -

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Basic information

Entry
Database: PDB / ID: 4v45
TitleE. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE
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. / 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 / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJuers, D.H. / McCarter, J.D. / Withers, S.G. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2001
Title: A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase
Authors: Juers, D.H. / Heightman, T.D. / Vasella, A. / McCarter, J.D. / Mackenzie, L. / Withers, S.G. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 2000
Title: High Resolution Structure 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.
#2: 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.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of beta-galactosidase from Escherichia coli
Authors: Jacobson, R.H. / Matthews, B.W.
History
DepositionSep 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1JZ0, 1JZ1
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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.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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Beta-Galactosidase
F: Beta-Galactosidase
G: Beta-Galactosidase
H: Beta-Galactosidase
I: Beta-Galactosidase
J: Beta-Galactosidase
K: Beta-Galactosidase
L: Beta-Galactosidase
M: Beta-Galactosidase
N: Beta-Galactosidase
O: Beta-Galactosidase
P: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,871,62296
Polymers1,867,19416
Non-polymers4,42880
Water40,3542240
1
A: Beta-Galactosidase
B: Beta-Galactosidase
C: Beta-Galactosidase
D: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,90624
Polymers466,7994
Non-polymers1,10720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Beta-Galactosidase
F: Beta-Galactosidase
G: Beta-Galactosidase
H: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,90624
Polymers466,7994
Non-polymers1,10720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Beta-Galactosidase
J: Beta-Galactosidase
K: Beta-Galactosidase
L: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,90624
Polymers466,7994
Non-polymers1,10720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Beta-Galactosidase
N: Beta-Galactosidase
O: Beta-Galactosidase
P: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,90624
Polymers466,7994
Non-polymers1,10720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.500, 207.200, 510.200
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Beta-Galactosidase / E.C.3.2.1.23 / LACTASE / lacZ / beta-d-galactosidase /


Mass: 116699.641 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): A324 / References: UniProt: P00722, beta-galactosidase
#2: Sugar
ChemComp-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose / 2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE / 2-deoxy-2-fluoro-beta-D-galactose / 2-deoxy-2-fluoro-D-galactose / 2-deoxy-2-fluoro-galactose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: 16 FOLD CONSTRAINED NCS WAS USED
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: Cacodylate, PEG 8000, MgSO4, NaCl, BME, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 295K, pH 5.90

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 21, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→68.5 Å / Num. all: 523624 / Num. obs: 523624 / % possible obs: 70 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
TNTrefinement
WEISdata reduction
CCP4data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F49

1f49
PDB Unreleased entry


Resolution: 2.6→68.5 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT / Details: 16 FOLD CONSTRAINED NCS WAS USED
RfactorNum. reflection% reflectionSelection details
all0.23 523624 --
obs0.23 523624 70 %-
Rfree---RANDOM
Solvent computationSolvent model: BABINET PRINCIPLE / Bsol: 200 Å2 / ksol: 0.8 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.8 Å20 Å2-187.3 Å2
2--6.2 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→68.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms65752 0 120 1120 66992
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0171355841.1
X-RAY DIFFRACTIONt_angle_deg2.6181839042
X-RAY DIFFRACTIONt_dihedral_angle_d19.6779520
X-RAY DIFFRACTIONt_incorr_chiral_ct00
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.01137122
X-RAY DIFFRACTIONt_gen_planes0.015196646
X-RAY DIFFRACTIONt_it5.31355681
X-RAY DIFFRACTIONt_nbd0.045238810

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