+Open data
-Basic information
Entry | Database: PDB / ID: 1nxo | ||||||
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Title | MicArec pH7.0 | ||||||
Components | DNA-binding response regulator | ||||||
Keywords | SIGNALING PROTEIN / doubly wound 5 alpha 5 beta fold | ||||||
Function / homology | Function and homology information phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Bent, C.J. / Isaacs, N.W. / Mitchell, T.J. / Riboldi-Tunnicliffe, A. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2004 Title: Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states. Authors: Bent, C.J. / Isaacs, N.W. / Mitchell, T.J. / Riboldi-Tunnicliffe, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nxo.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxo.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxo ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxo | HTTPS FTP |
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-Related structure data
Related structure data | 1nxpC 1nxtSC 1nxwC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The second part of the biological assembly is generated by the two fold axis: x, -y, -z |
-Components
#1: Protein | Mass: 13600.730 Da / Num. of mol.: 1 / Fragment: MicA receiver domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PET33B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S1K0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40%v/v PEG 300, 5%w/v PEG 1,000, 100mM Tris, , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40.16 Å / Num. all: 19291 / Num. obs: 12010 / % possible obs: 99.43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.22 Å2 / Rsym value: 0.084 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.85→1.898 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.537 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 260225 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.237 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NXT Resolution: 1.85→40.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.43 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.223 / ESU R Free: 0.127 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 15.055 Å / Origin y: 35.368 Å / Origin z: 5.533 Å
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Refinement TLS group |
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Refinement | *PLUS Rfactor Rfree: 0.2181 / Rfactor Rwork: 0.1659 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.314 / Rfactor Rwork: 0.236 |