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Yorodumi- PDB-4rww: Crystal Structure of L. monocytogenes PstA in complex with cyclic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rww | ||||||
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Title | Crystal Structure of L. monocytogenes PstA in complex with cyclic-di-AMP | ||||||
Components | Lmo2692 protein | ||||||
Keywords | PROTEIN BINDING / PII-like | ||||||
Function / homology | Function and homology information Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Choi, P.H. / Tong, L. | ||||||
Citation | Journal: Microbiologyopen / Year: 2015 Title: Molecular basis for the recognition of cyclic-di-AMP by PstA, a PII -like signal transduction protein. Authors: Choi, P.H. / Sureka, K. / Woodward, J.J. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rww.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rww.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rww ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rww | HTTPS FTP |
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-Related structure data
Related structure data | 4rwxC 3m05S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12343.028 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo2692 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3Y7 #2: Chemical | ChemComp-2BA / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 54378 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.2 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M05 Resolution: 1.6→29.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.36 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.077 / 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: 16.624 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.58 Å
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