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- PDB-2gbp: SUGAR AND SIGNAL-TRANSDUCER BINDING SITES OF THE ESCHERICHIA COLI... -

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Basic information

Entry
Database: PDB / ID: 2gbp
TitleSUGAR AND SIGNAL-TRANSDUCER BINDING SITES OF THE ESCHERICHIA COLI GALACTOSE CHEMORECEPTOR PROTEIN
ComponentsD-GALACTOSE/D-GLUCOSE BINDING PROTEIN
KeywordsPERIPLASMIC BINDING PROTEIN
Function / homology
Function and homology information


methylgalactoside transport / galactose transmembrane transport / carbohydrate transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / periplasmic space / calcium ion binding / metal ion binding / membrane
Similarity search - Function
D-galactose-binding periplasmic protein MglB-like, PBP domain / : / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / D-galactose-binding periplasmic protein / D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsVyas, N.K. / Vyas, M.N. / Quiocho, F.A.
Citation
Journal: Science / Year: 1988
Title: Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein.
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#1: Journal: Nature / Year: 1987
Title: A Novel Calcium Binding Site in the Galactose-Binding Protein of Bacterial Transport and Chemotaxis
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: The 3 Angstroms Resolution Structure of a D-Galactose-Binding Protein for Transport and Chemotaxis in Escherichia Coli
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Preliminary Crystallographic Data of Receptors for Transport and Chemotaxis in Escherichia Coli. D-Galactose and Maltose-Binding Proteins
Authors: Quiocho, F.A. / Meador, W.E. / Pflugrath, J.W.
History
DepositionFeb 23, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-GALACTOSE/D-GLUCOSE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6283
Polymers33,4081
Non-polymers2202
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.000, 37.050, 61.570
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-GALACTOSE/D-GLUCOSE BINDING PROTEIN


Mass: 33407.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02927, UniProt: P0AEE5*PLUS
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal grow
*PLUS
pH: 4.9 / Method: microdialysis
Details: referred to 'Quiocho, F.A.', (1979) J.Mol.Biol., 133, 181-184
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein11
213 %(w/v)PEG11
340 mM11NaCl
46 mMsodium citrate 11
514 %(w/v)PEG600012
640 mM12NaCl
76 mMsodium citrate12

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→10 Å /
RfactorNum. reflection
obs0.146 19531
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 13 214 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.015
X-RAY DIFFRACTIONp_angle_d0.0450.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.811.5
X-RAY DIFFRACTIONp_mcangle_it2.862
X-RAY DIFFRACTIONp_scbond_it4.392.5
X-RAY DIFFRACTIONp_scangle_it63
X-RAY DIFFRACTIONp_plane_restr0.0120.01
X-RAY DIFFRACTIONp_chiral_restr0.10.05
X-RAY DIFFRACTIONp_singtor_nbd0.1970.5
X-RAY DIFFRACTIONp_multtor_nbd0.2010.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.63
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. reflection all: 19531 / Rfactor all: 0.146 / σ(I): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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