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- PDB-1pbp: FINE TUNING OF THE SPECIFICITY OF THE PERIPLASMIC PHOSPHATE TRANS... -

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Basic information

Entry
Database: PDB / ID: 1pbp
TitleFINE TUNING OF THE SPECIFICITY OF THE PERIPLASMIC PHOSPHATE TRANSPORT RECEPTOR: SITE-DIRECTED MUTAGENESIS, LIGAND BINDING, AND CRYSTALLOGRAPHIC STUDIES
ComponentsPHOSPHATE-BINDING PROTEIN
KeywordsPHOSPHATE TRANSPORT
Function / homology
Function and homology information


regulation of phosphatase activity / phosphate ion transport / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / outer membrane-bounded periplasmic space / DNA damage response / membrane
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWang, Z. / Choudhary, A. / Ledvina, P.S. / Quiocho, F.A.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Fine tuning the specificity of the periplasmic phosphate transport receptor. Site-directed mutagenesis, ligand binding, and crystallographic studies.
Authors: Wang, Z. / Choudhary, A. / Ledvina, P.S. / Quiocho, F.A.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Th E Immunodominant 38-kDa Lipoprotein Antigen of Mycobacterium Tuberculosis is a Phosphate-Binding Protein
Authors: Chang, Z. / Choudhary, A. / Lathigra, R. / Quiocho, F.A.
#2: Journal: Nature / Year: 1990
Title: High Specificity of a Phosphate Transport Protein Determined by Hydrogen Bonds
Authors: Luecke, H. / Quiocho, F.A.
History
DepositionJul 20, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: 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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5672
Polymers34,4721
Non-polymers951
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.880, 64.570, 124.670
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 PHOSPHATE-BINDING PROTEIN


Mass: 34471.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P06128, UniProt: P0AG82*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.25 mg/mlprotein1drop
21.5 mMpotassium phosphate1drop
313.5 %(w/v)PEG60001drop
437.5 mM1dropKCl
515 mMpotassium acetate1drop
618 %(w/v)PEG60001reservoir
750 mM1reservoirKCl
82 mMpotassium phosphate1reservoir
920 mMpotassium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 22300 / % possible obs: 69.5 % / Observed criterion σ(F): 0
Reflection
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 1.9 Å / Num. all: 38401 / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.0447

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.147 --
obs0.147 38401 69.5 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 5 214 2658
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONx_bond_d0.0170.06
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_deg1.84910
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.849 / Weight: 10

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