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Open data
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Basic information
Entry | Database: PDB / ID: 1a40 | ||||||
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Title | PHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP | ||||||
![]() | PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR | ||||||
![]() | PHOSPHATE-BINDING PROTEIN / MUTAGENESIS / CHARGE COMPLEMENTARY / KINETICS | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ledivina, P.S. / Wang, Z. / Tsai, A. / Koehl, E. / Quiocho, F.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Negative Electrostatic Surface Potential of Protein Sites Specific for Anionic Ligands Authors: Ledvina, P.S. / Yao, N. / Choudhary, A. / Quiocho, F.A. #3: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
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Full document | ![]() | 428.6 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2abhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34572.730 Da / Num. of mol.: 1 / Mutation: A197W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 8.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.78 Å |