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Yorodumi- PDB-7u9h: Crystal Structure of Escherichia coli apo Pyridoxal 5'-phosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u9h | |||||||||
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Title | Crystal Structure of Escherichia coli apo Pyridoxal 5'-phosphate homeostasis protein (YGGS) | |||||||||
Components | Pyridoxal phosphate homeostasis protein | |||||||||
Keywords | 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 phosphate homeostasis protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Donkor, A.K. / Ghatge, M.S. / Musayev, F.N. / Safo, M.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u9h.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u9h.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/7u9h ftp://data.pdbj.org/pub/pdb/validation_reports/u9/7u9h | HTTPS FTP |
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-Related structure data
Related structure data | 7u9cC 7uatC 7uauC 7uaxC 7ub4C 7ub8C 7ubpC 7ubqC 1w8gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Escherichia coli (E. coli) / Gene: yggS, yggS_1 / Plasmid: pET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: C3SV52 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2M Ammonium sulfate, 5% Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 2, 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→28.503 Å / Num. obs: 22173 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.018 / Rrim(I) all: 0.071 / Net I/σ(I): 33 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1w8g Resolution: 2→28.503 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.97 / 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: 78.34 Å2 / Biso mean: 32.4521 Å2 / Biso min: 17.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→28.503 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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