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- PDB-1ixh: PHOSPHATE-BINDING PROTEIN (PBP) COMPLEXED WITH PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1ixh
TitlePHOSPHATE-BINDING PROTEIN (PBP) COMPLEXED WITH PHOSPHATE
ComponentsPHOSPHATE-BINDING PROTEIN
KeywordsPHOSPHATE TRANSPORT / ULTRA HIGH RESOLUTION / PHOSPHATE BINDIN PROTEIN
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 domain / PBP superfamily 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsWang, Z. / Luecke, H. / Quiocho, F.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: A low energy short hydrogen bond in very high resolution structures of protein receptor--phosphate complexes.
Authors: Wang, Z. / Luecke, H. / Yao, N. / Quiocho, F.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Negative Electrostatic Surface Potential of Protein Sites Specific for Anionic Ligands
Authors: Ledvina, P.S. / Yao, N. / Choudhary, A. / Quiocho, F.A.
#2: Journal: Biochemistry / Year: 1996
Title: Modulation of a Salt Link Does not Affect Binding of Phosphate to its Specific Active Transport Receptor
Authors: Yao, N. / Ledvina, P.S. / Choudhary, A. / Quiocho, F.A.
#3: 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.
#4: Journal: J.Biol.Chem. / Year: 1994
Title: The Immunodominant 38-kDa Lipoprotein Antigen of Mycobacterium Tuberculosis is a Phosphate-Binding Protein
Authors: Chang, Z. / Choudhary, A. / Lathigra, R. / Quiocho, F.A.
#5: Journal: Nature / Year: 1990
Title: High Specificity of a Phosphate Transport Protein Determined by Hydrogen Bonds
Authors: Luecke, H. / Quiocho, F.A.
History
DepositionAug 1, 1996Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)34,5532
Polymers34,4581
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.506, 63.379, 122.373
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: 34457.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAN92 / Cell line: AN1667 / Cellular location: PERIPLASM / Gene: PHO-S / Cell line (production host): AN1667 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): PIBI24 / References: UniProt: P06128, UniProt: P0AG82*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Wang, Z., (1994) J.Biol.Chem., 269, 25091.
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDetector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 0.98→19.4 Å / Num. obs: 147105 / % possible obs: 79.8 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 35.3
Reflection shellResolution: 0.98→1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.6 / % possible all: 29.8

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Processing

Software
NameClassification
SHELXL-96model building
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ABH

1abh
PDB Unreleased entry


Resolution: 0.98→19.4 Å / Num. parameters: 28413 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.141 14445 10 %
all0.117 144454 -
obs0.114 -79.8 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 547 / Occupancy sum non hydrogen: 3110
Refinement stepCycle: LAST / Resolution: 0.98→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 5 0 2453

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