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- PDB-3gbp: STRUCTURE OF THE PERIPLASMIC GLUCOSE/GALACTOSE RECEPTOR OF SALMON... -

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Basic information

Entry
Database: PDB / ID: 3gbp
TitleSTRUCTURE OF THE PERIPLASMIC GLUCOSE/GALACTOSE RECEPTOR OF SALMONELLA TYPHIMURIUM
ComponentsGALACTOSE-BINDING PROTEIN
KeywordsPERIPLASMIC BINDING PROTEIN
Function / homology
Function and homology information


chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / metal ion binding
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/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMowbray, S.L.
Citation
Journal: Receptor / Year: 1990
Title: Structure of the periplasmic glucose/galactose receptor of Salmonella typhimurium.
Authors: Mowbray, S.L. / Smith, R.D. / Cole, L.B.
#1: Journal: Mol.Gen.Genet. / Year: 1988
Title: The Mg1B Sequence of Salmonella Typhimurium Lt2; Promoter Analysis by Gene Fusions and Evidence for a Divergently Oriented Gene Coding for the Mg1 Repressor
Authors: Benner-Luger, D. / Boos, W.
#2: Journal: J.Biol.Chem. / Year: 1983
Title: The X-Ray Structure of the Periplasmic Galactose Binding Protein from Salmonella Typhimurium at 3.0-A Resolution
Authors: Mowbray, S.L. / Petsko, G.A.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: The Introduction of Specific Sites for Heavy Metal Binding in a Crystalline Protein
Authors: Mowbray, S.L. / Petsko, G.A.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Preliminary X-Ray Data for the Galactose Binding Protein from Salmonella Typhimurium
Authors: Alber, T. / Fahnestock, M. / Mowbray, S.L. / Petsko, G.A.
History
DepositionJan 25, 1990Processing site: BNL
SupersessionJul 15, 1991ID: 1GBP
Revision 1.0Jul 15, 1991Provider: 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _pdbx_validate_close_contact.auth_atom_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: GALACTOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4243
Polymers33,2031
Non-polymers2202
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.590, 37.280, 80.230
Angle α, β, γ (deg.)90.00, 123.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GALACTOSE-BINDING PROTEIN


Mass: 33203.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P23905
#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.: 106 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal grow
*PLUS
Method: other / Details: Mowbray, S.L., (1983) J. Biol. Chem., 258, 7991.

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 7.5 Å / Num. obs: 10378 / Rmerge(I) obs: 0.114

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.158 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 25 318 3195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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