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- PDB-1gcg: THE 1.9 ANGSTROMS X-RAY STRUCTURE OF A CLOSED UNLIGANDED FORM OF ... -

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Basic information

Entry
Database: PDB / ID: 1gcg
TitleTHE 1.9 ANGSTROMS X-RAY STRUCTURE OF A CLOSED UNLIGANDED FORM OF THE PERIPLASMIC GLUCOSE(SLASH)GALACTOSE RECEPTOR FROM SALMONELLA TYPHIMURIUM
ComponentsGALACTOSE/GLUCOSE-BINDING PROTEIN
KeywordsGALACTOSE-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
D-galactose/methyl-galactoside binding periplasmic protein MglB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsFlocco, M.M. / Mowbray, S.L.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: The 1.9 A x-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium.
Authors: Flocco, M.M. / Mowbray, S.L.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: The 1.7 Angstroms Refined X-Ray Structure of the Periplasmic Glucose(Slash)Galactose Receptor from Salmonella Typhimurium
Authors: Zou, J.-Y. / Flocco, M.M. / Mowbray, S.L.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Ribose and Glucose-Galactose Receptors Competitors in Bacterial Chemotaxis
Authors: Mowbray, S.L.
#3: Journal: Receptor / Year: 1990
Title: Structure of the Periplasmic Glucose(Slash)Galactose Receptor of Salmonella Typhimurium
Authors: Mowbray, S.L. / Smith, R.D. / Cole, L.B.
#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
DepositionFeb 3, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,5012
Polymers33,4611
Non-polymers401
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.140, 37.020, 80.630
Angle α, β, γ (deg.)90.00, 123.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GALACTOSE/GLUCOSE-BINDING PROTEIN


Mass: 33460.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P23905
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SEE REFERENCE 3. SWISS- ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SEE REFERENCE 3. SWISS-PROT ENTRY NAME: DGAL_SALTY SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ ALA 175 HIS 152

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal grow
*PLUS
Method: other / Details: used as seeds
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MTris-HCl1reservoir
40.2 Msodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 58.6 Å / Num. all: 21036 / % possible obs: 59612 % / Observed criterion σ(I): 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→7.5 Å / σ(F): 1
Details: RESIDUE ASP 212, WHOSE OD1 ATOM IS IN CLOSE CONTACT WITH THR 253 OG1, IS A BURIED ASPARTATE AND THIS FACT HAS BEEN DISCUSSED IN REFERENCE 1.
RfactorNum. reflection
Rwork0.179 -
obs0.179 20142
Refinement stepCycle: LAST / Resolution: 1.9→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 1 525 3419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.44
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

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