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- PDB-4v44: E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE -

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Basic information

Entry
Database: PDB / ID: 4v44
TitleE. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE
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-lactose / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: 1JYY, 1JYZ
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Oct 16, 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)1,874,21696
Polymers1,867,19416
Non-polymers7,02280
Water46,6952592
1
A: Beta-Galactosidase
B: Beta-Galactosidase
C: Beta-Galactosidase
D: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,55424
Polymers466,7994
Non-polymers1,75620
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)468,55424
Polymers466,7994
Non-polymers1,75620
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)468,55424
Polymers466,7994
Non-polymers1,75620
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)468,55424
Polymers466,7994
Non-polymers1,75620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.600, 207.300, 510.300
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): JM109 / References: UniProt: P00722, beta-galactosidase
#2: Polysaccharide
2-deoxy-2-fluoro-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 2-deoxy-2-fluoro-beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 344.288 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2-deoxy-2-fluoro-beta-lactose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5_2*F]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp2fluoro]{}}LINUCSPDB-CARE
#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.: 2592 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
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 22, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 409961 / Num. obs: 409961 / % possible obs: 66 % / Redundancy: 1.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.74 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / Num. unique all: 18525 / % possible all: 37.9

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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: 2.7→20 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
Rwork0.234 ---
all0.234 409961 --
obs0.234 409961 66 %-
Rfree---RANDOM
Solvent computationSolvent model: BABINET PRINCIPLE / Bsol: 200 Å2 / ksol: 0.8 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.9 Å20 Å2-174.6 Å2
2--7.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms65752 0 216 1296 67264
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0151357761.1
X-RAY DIFFRACTIONt_angle_deg2.361842242
X-RAY DIFFRACTIONt_dihedral_angle_d19.7779520
X-RAY DIFFRACTIONt_incorr_chiral_ct00
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.00837122
X-RAY DIFFRACTIONt_gen_planes0.013196646
X-RAY DIFFRACTIONt_it2.41357766
X-RAY DIFFRACTIONt_nbd0.038272810

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