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- PDB-2abh: PHOSPHATE-BINDING PROTEIN (RE-REFINED) -

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Basic information

Entry
Database: PDB / ID: 2abh
TitlePHOSPHATE-BINDING PROTEIN (RE-REFINED)
ComponentsPHOSPHATE-BINDING PROTEIN
KeywordsPHOSPHOTRANSFERASE / 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 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 / Resolution: 1.7 Å
AuthorsYao, N. / Choudhary, A. / Ledvina, P.S. / Quiocho, F.A.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Fine Tuning the Specificity of the Periplasmic Phosphate Transport Receptor
Authors: Wang, Z. / Choudhary, A. / Ledvina, P.S. / 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
DepositionNov 28, 1995Processing site: BNL
SupersessionApr 21, 1997ID: 1ABH
Revision 1.0Apr 21, 1997Provider: 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_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

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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)34,5532
Polymers34,4581
Non-polymers951
Water3,405189
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: 34457.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: PAN92 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
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

Diffraction sourceWavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 36946 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.765 % / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 1.7→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.177 -
obs0.177 36051
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 5 189 2632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.608
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 Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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