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- PDB-4ttg: Beta-galactosidase (E. coli) in the presence of potassium chloride. -

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Basic information

Entry
Database: PDB / ID: 4ttg
TitleBeta-galactosidase (E. coli) in the presence of potassium chloride.
ComponentsBeta-galactosidase
KeywordsHYDROLASE / glycosidase / (alpha/beta)8 barrel / jelly roll / immunoglobulin / beta supersandwich / complex with potassium
Function / homology
Function and homology information


lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion 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
: / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJuers, D.H.
CitationJournal: Phys Chem Chem Phys / Year: 2015
Title: Elucidating factors important for monovalent cation selectivity in enzymes: E. coli beta-galactosidase as a model.
Authors: Wheatley, R.W. / Juers, D.H. / Lev, B.B. / Huber, R.E. / Noskov, S.Y.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_related ...entity_src_gen / pdbx_database_related / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.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_conn_type.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)477,468167
Polymers466,1534
Non-polymers11,315163
Water80,1854451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50380 Å2
ΔGint143 kcal/mol
Surface area135780 Å2
MethodPISA
2
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,34191
Polymers233,0772
Non-polymers6,26589
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20130 Å2
ΔGint65 kcal/mol
Surface area73480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.290, 168.100, 200.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-galactosidase / Beta-gal / Lactase


Mass: 116538.266 Da / Num. of mol.: 4 / Fragment: UNP residues 15-1029
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VNN2, beta-galactosidase

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Non-polymers , 5 types, 4614 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4451 / 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: 54.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris 100 mM NaCl 200 mM MgCl2 9-12 % PEG 8000 Microseeded Serial soaked in buffer with 100 mM KCl, yielding 100 mM KCl and 16 nM NaCl Cryoprotected by serial soaks over several ...Details: 100 mM Bis-Tris 100 mM NaCl 200 mM MgCl2 9-12 % PEG 8000 Microseeded Serial soaked in buffer with 100 mM KCl, yielding 100 mM KCl and 16 nM NaCl Cryoprotected by serial soaks over several hours in 5% increments to 30%/70% (v/v) DMSO/above KCl buffer Cooled in the nitrogen stream at 100 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→56.5 Å / Num. obs: 604015 / % possible obs: 92.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.7 / % possible all: 87.5

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DP0

1dp0


Resolution: 1.6→55.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.259 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.188 8778 1.5 %RANDOM
Rwork0.15979 ---
obs0.1602 595237 92.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0 Å2
2--0.27 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.6→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32632 0 559 4451 37642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01934863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.91347614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81954302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34223.7011797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.916155391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97315275
X-RAY DIFFRACTIONr_chiral_restr0.1530.25078
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02127475
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.59854
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 547 -
Rwork0.221 36739 -
obs--78.82 %

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