+Open data
-Basic information
Entry | Database: PDB / ID: 4zlx | ||||||
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Title | N-terminal DNA binding domain of the antitoxin Phd from phage P1 | ||||||
Components | Antitoxin phd | ||||||
Keywords | TRANSCRIPTION / transcription factor / toxin-antitoxin / DNA binding / intrinsic disorder / conditional cooperativity | ||||||
Function / homology | Function and homology information toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Garcia-Pino, A. / Loris, R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation. Authors: Garcia-Pino, A. / De Gieter, S. / Talavera, A. / De Greve, H. / Efremov, R.G. / Loris, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zlx.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zlx.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zlx_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 4zlx_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 4zlx_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 4zlx_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zlx ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zlx | HTTPS FTP |
-Related structure data
Related structure data | 4zm0C 4zm2C 3hs2S 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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-Components
#1: Protein | Mass: 6169.816 Da / Num. of mol.: 2 / Fragment: UNP residues 1-45 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: phd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06253 #2: Chemical | ChemComp-ACT / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 200 mM Lithium Sulfate monohydrate, 20% w/v PEG3350 PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→29.9 Å / Num. obs: 4518 / % possible obs: 97.3 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.14 Å2 / Net I/σ(I): 57.8 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 17.9 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HS2 Resolution: 2.31→29.86 Å / Cor.coef. Fo:Fc: 0.9335 / Cor.coef. Fo:Fc free: 0.8965 / SU R Cruickshank DPI: 0.329 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.338 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.241
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Displacement parameters | Biso mean: 32.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.302 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.58 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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