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- PDB-1sbp: 1.7 ANGSTROMS REFINED STRUCTURE OF SULFATE-BINDING PROTEIN INVOLV... -

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Basic information

Entry
Database: PDB / ID: 1sbp
Title1.7 ANGSTROMS REFINED STRUCTURE OF SULFATE-BINDING PROTEIN INVOLVED IN ACTIVE TRANSPORT AND NOVEL MODE OF SULFATE BINDING
ComponentsSULFATE-BINDING PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


sulfur compound metabolic process / sulfate transmembrane transport / sulfate binding / molecular carrier activity / outer membrane-bounded periplasmic space / extracellular space
Similarity search - Function
Sulphate/thiosulphate-binding, conserved site / Prokaryotic sulfate-binding proteins signature 1. / Sulphate/thiosulphate-binding site / Prokaryotic sulfate-binding proteins signature 2. / Thiosulphate/Sulfate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfate-binding protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSack, J.S. / Quiocho, F.A.
Citation
Journal: Protein Sci. / Year: 1993
Title: Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein.
Authors: He, J.J. / Quiocho, F.A.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Engineered Interdomain Disulfide in the Periplasmic Receptor for Sulfate Transport Reduces Flexibility. Site-Directed Mutagenesis and Ligand-Binding Studies
Authors: Jacobson, B.L. / He, J.J. / Vermersch, P.S. / Lemon, D.D. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: The 2 Angstroms Resolution Structure of the Sulfate-Binding Protein Involved in Active Transport in Salmonella Typhimurium
Authors: Pflugrath, J.W. / Quiocho, F.A.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Sulfate-Binding Protein Dislikes Protonated Oxyacids. A Molecular Explanation
Authors: Jacobson, B.L. / Quiocho, F.A.
#4: Journal: Nature / Year: 1985
Title: Sulphate Sequestered in the Sulphate-Binding Protein of Salmonella Typhimurium is Bound Solely by Hydrogen Bonds
Authors: Pflugrath, J.W. / Quiocho, F.A.
#5: Journal: J.Biol.Chem. / Year: 1980
Title: Amino Acid Sequence of the Sulfate-Binding Protein from Salmonella Typhimurium Lt2
Authors: Isihara, H. / Hogg, R.W.
History
DepositionJul 19, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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

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Assembly

Deposited unit
A: SULFATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6262
Polymers34,5301
Non-polymers961
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.770, 49.370, 141.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SULFATE-BINDING PROTEIN


Mass: 34529.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P02906
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion / Details: Wilson, D.K., (1988) J.Mol.Biol., 200, 613.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
250 mM1dropKCl
350 mMsodium citrate1drop
47.5 %PEG60001drop
515 %PEG60001reservoir

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.178 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 5 138 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.041
X-RAY DIFFRACTIONp_mcangle_it1.5891.5
X-RAY DIFFRACTIONp_scbond_it1.4671
X-RAY DIFFRACTIONp_scangle_it2.3791.5
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.2160.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.5
X-RAY DIFFRACTIONp_multtor_nbd0.1880.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1770.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.23
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor21.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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