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- PDB-1ixg: PHOSPHATE-BINDING PROTEIN MUTANT WITH THR 141 REPLACED BY ASP (T1... -

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Basic information

Entry
Database: PDB / ID: 1ixg
TitlePHOSPHATE-BINDING PROTEIN MUTANT WITH THR 141 REPLACED BY ASP (T141D), COMPLEXED WITH PHOSPATE
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: 1.05 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.645, 63.493, 123.788
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 / Mutation: T141D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAN92 / Cell line: AN2538 / Cellular location: PERIPLASM / Gene: PHO-S / Cell line (production host): AN2538 / 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: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.05→28.1 Å / Num. obs: 111988 / % possible obs: 71.7 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.5
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 3.8 / % possible all: 32.2

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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 1PBP

1pbp


Resolution: 1.05→28.1 Å / Num. parameters: 28566 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.139 11169 10 %EVERY 10TH REFLECTION
all0.112 111699 --
obs0.109 -71.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 546 / Occupancy sum non hydrogen: 3120.5
Refinement stepCycle: LAST / Resolution: 1.05→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 5 0 2454

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