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- PDB-1a40: PHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP -

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Basic information

Entry
Database: PDB / ID: 1a40
TitlePHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP
ComponentsPHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR
KeywordsPHOSPHATE-BINDING PROTEIN / MUTAGENESIS / CHARGE COMPLEMENTARY / KINETICS
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLedivina, P.S. / Wang, Z. / Tsai, A. / Koehl, E. / Quiocho, F.A.
Citation
Journal: Protein Sci. / Year: 1998
Title: Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: equilibrium, kinetic, and crystallographic studies.
Authors: Ledvina, P.S. / Tsai, A.L. / Wang, Z. / Koehl, E. / Quiocho, F.A.
#1: 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.
#2: 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.
#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.
History
DepositionFeb 10, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: 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 1.4Aug 2, 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 PERIPLASMIC PROTEIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6682
Polymers34,5731
Non-polymers951
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.410, 62.760, 122.730
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 PERIPLASMIC PROTEIN PRECURSOR / PBP A197W


Mass: 34572.730 Da / Num. of mol.: 1 / Mutation: A197W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PAN92 / Production host: Escherichia coli (E. coli) / Strain (production host): PET-22B / 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.: 411 / 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: 2.3 Å3/Da / Density % sol: 46.65 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.5 mg/mlprotein1drop
215 mMpotassium phosphate1drop
320 %(w/v)PEG60001reservoir
450 mM1reservoirKCl
52 mMpotassium phosphate1reservoir
620 mMpotassium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 35260 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.086 / Net I/σ(I): 8
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.314 / % possible all: 63.6
Reflection
*PLUS
Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 63.6 % / Rmerge(I) obs: 0.314

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABH

2abh


Resolution: 1.7→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3344 10 %RANDOM
Rwork0.203 ---
obs0.203 33200 92.3 %-
Displacement parametersBiso mean: 8.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 5 411 2863
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_deg1.661
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.78
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.552
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 / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.78
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.552
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.78 Å

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