+Open data
-Basic information
Entry | Database: PDB / ID: 4ae5 | ||||||
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Title | STRUCTURE OF A MAJOR REGULATOR OF STAPHYLOCOCCAL PATHOGENESIS | ||||||
Components | SIGNAL TRANSDUCTION PROTEIN TRAP | ||||||
Keywords | SIGNALING PROTEIN / PHOSPHORYLATION / RNAIII / RAP / QUORUM SENSING / BIOFILM / TOXIN PRODUCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Hirshberg, M. / Henrick, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of the Signal Transduction Protein Trap (Target of Rnaiii-Activating Protein). Authors: Henrick, K. / Hirshberg, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ae5.cif.gz | 273.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ae5.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ae5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ae5_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 4ae5_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 4ae5_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 4ae5_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4ae5 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4ae5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19574.729 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: RN6390B / References: UniProt: Q7A4W3, UniProt: Q2G2F3*PLUS #2: Chemical | ChemComp-FMT / #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: 2.3 Å3/Da / Density % sol: 46.55 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.66 Details: HANGING DROP, 18 DEGREES CELCIUS, 18% PEG 4K, 0.050 M NACIT PH 5.66, 1% PEG 500 MME, PROTEIN IN DROP 4.4MG/ML DROP 1:1, CRYOPROTECTANT USED: 20% PEG 4K, 0.050 M NA CITRATE PH 5.66, 1% PEG 500 MME, 35% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.2445 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2445 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→74.5 Å / Num. obs: 60732 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.23 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.09 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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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: 19.029 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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