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- PDB-1glg: CRYSTALLOGRAPHIC ANALYSIS OF THE EPIMERIC AND ANOMERIC SPECIFICIT... -

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Basic information

Entry
Database: PDB / ID: 1glg
TitleCRYSTALLOGRAPHIC ANALYSIS OF THE EPIMERIC AND ANOMERIC SPECIFICITY OF THE PERIPLASMIC TRANSPORT(SLASH)CHEMOTACTIC PROTEIN RECEPTOR FOR D-GLUCOSE AND D-GALACTOSE
ComponentsGALACTOSE/GLUCOSE-BINDING PROTEIN
KeywordsGALACTOSE-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-galactopyranose / 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: 2 Å
AuthorsVyas, M.N. / Vyas, N.K. / Quiocho, F.A.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic analysis of the epimeric and anomeric specificity of the periplasmic transport/chemosensory protein receptor for D-glucose and D-galactose.
Authors: Vyas, M.N. / Vyas, N.K. / Quiocho, F.A.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Comparison of the Periplasmic Receptors for L-Arabinose, D-Galactose, and D-Ribose
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#2: Journal: Science / Year: 1988
Title: Sugar and Signal-Transducer Binding Sites of the Escherichia Coli Galactose Receptor Protein
Authors: Vyas, N.K. / Vyas, M.N. / Quiocho, F.A.
#3: 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.
History
DepositionDec 27, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.process_site / _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 1.4Feb 7, 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: GALACTOSE/GLUCOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6283
Polymers33,4081
Non-polymers2202
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.980, 37.090, 61.900
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GALACTOSE/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-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG 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.: 215 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal grow
*PLUS
Method: other / Details: Quiocho, F.A., (1979) J. Mol. Biol., 133, 181.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 19700 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.167 12145
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 13 215 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.015
X-RAY DIFFRACTIONp_angle_d0.0380.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.971
X-RAY DIFFRACTIONp_mcangle_it1.61.5
X-RAY DIFFRACTIONp_scbond_it1.381.5
X-RAY DIFFRACTIONp_scangle_it2.142
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.0550.05
X-RAY DIFFRACTIONp_singtor_nbd0.1950.5
X-RAY DIFFRACTIONp_multtor_nbd0.1890.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1530.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor8.53
X-RAY DIFFRACTIONp_staggered_tor20.915
X-RAY DIFFRACTIONp_orthonormal_tor33.320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.94 Å2

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