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- PDB-7u9c: Crystal Structure of the wild type Escherichia coli Pyridoxal 5'-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u9c | |||||||||
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Title | Crystal Structure of the wild type Escherichia coli Pyridoxal 5'-phosphate homeostasis protein (YGGS) | |||||||||
![]() | Pyridoxal phosphate homeostasis protein | |||||||||
![]() | PROTEIN TRANSPORT / PLP-binding protein / Vitamin B6 / PLP homeostasis | |||||||||
Function / homology | Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / PLP-binding barrel / pyridoxal phosphate binding / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxal phosphate homeostasis protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Donkor, A.K. / Ghatge, M.S. / Safo, M.K. / Musayev, F.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability. Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / ...Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / Safo, M.K. / Contestabile, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.9 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u9hC ![]() 7uatC ![]() 7uauC ![]() 7uaxC ![]() 7ub4C ![]() 7ub8C ![]() 7ubpC ![]() 7ubqC ![]() 1w8gS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25820.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES/NaOH pH 7.5, 0.8 NaH2PO4/0.8M KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 11, 2021 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→29.271 Å / Num. obs: 19252 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 31.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Net I/σ(I): 30.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1w8g Resolution: 2.1→29.271 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.49 Å2 / Biso mean: 34.9622 Å2 / Biso min: 17.92 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→29.271 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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