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Yorodumi- PDB-7o4x: Crystal structure of the PII-like protein PotN from Lentilactobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o4x | ||||||
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Title | Crystal structure of the PII-like protein PotN from Lentilactobacillus hilgardii | ||||||
Components | Nitrogen regulatory protein P-II | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Lactobacillus brevis subsp. gravesensis ATCC 27305 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Heim, C. / Hartmann, M.D. | ||||||
Citation | Journal: Febs J. / Year: 2022 Title: PotN represents a novel energy-state sensing PII subfamily, occurring in firmicutes. Authors: Iskhakova, Z.I. / Zhuravleva, D.E. / Heim, C. / Hartmann, M.D. / Laykov, A.V. / Forchhammer, K. / Kayumov, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o4x.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o4x.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 7o4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o4x ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o4x | HTTPS FTP |
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-Related structure data
Related structure data | 2eg1S S: Starting model for refinement |
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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: 13759.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis subsp. gravesensis ATCC 27305 (bacteria) Gene: HMPREF0496_1931 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C2D309 |
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#2: Chemical | ChemComp-ADP / |
#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: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.56 M Tri-Na Citrate pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40.11 Å / Num. obs: 18721 / % possible obs: 100 % / Redundancy: 26.19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.093 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 24.71 % / Rmerge(I) obs: 2.03 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2935 / CC1/2: 0.72 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EG1 Resolution: 1.65→40.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.205 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→40.08 Å
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Refine LS restraints |
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