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- PDB-1ixi: PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMP... -

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Basic information

Entry
Database: PDB / ID: 1ixi
TitlePHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMPLEX WITH MONOBASIC PHOSPHATE ION
ComponentsPHOSPHATE-BINDING PROTEIN
KeywordsPHOSPHATE TRANSPORT / BINDING PROTEINS / PHOSPHATE-BINDING / MUTANT
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
DIHYDROGENPHOSPHATE ION / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIRECT PHASING FROM WILDTYPE STRUCTURE / Resolution: 1.89 Å
AuthorsWang, Z. / 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
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,5542
Polymers34,4571
Non-polymers971
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.970, 63.980, 123.970
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: 34456.613 Da / Num. of mol.: 1 / Mutation: D56N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAN92 / Description: PIBI24, INTERNATIONAL BIOTECHNOLOGIES / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / References: UniProt: P06128, UniProt: P0AG82*PLUS
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 49.05 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
pH: 4.5 / 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: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→8 Å / Num. obs: 22167 / % possible obs: 83.1 % / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.89→1.99 Å / % possible all: 63

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
UCSDdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: DIRECT PHASING FROM WILDTYPE STRUCTURE
Starting model: WILDTYPE STRUCTURE

Resolution: 1.89→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 -10 %RANDOM
Rwork0.2 ---
obs0.2 45850 83.1 %-
Refinement stepCycle: LAST / Resolution: 1.89→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 5 212 2655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.851
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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