[English] 日本語
Yorodumi- PDB-1ixi: PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ixi | ||||||
---|---|---|---|---|---|---|---|
Title | PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMPLEX WITH MONOBASIC PHOSPHATE ION | ||||||
Components | PHOSPHATE-BINDING PROTEIN | ||||||
Keywords | PHOSPHATE 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / DIRECT PHASING FROM WILDTYPE STRUCTURE / Resolution: 1.89 Å | ||||||
Authors | Wang, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ixi.cif.gz | 75 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ixi.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ixi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ixi_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ixi_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 1ixi_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1ixi_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ixi ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ixi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: 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 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 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
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 5, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.89→1.99 Å / % possible all: 63 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIRECT PHASING FROM WILDTYPE STRUCTURE Starting model: WILDTYPE STRUCTURE Resolution: 1.89→8 Å / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |