+Open data
-Basic information
Entry | Database: PDB / ID: 3zhi | ||||||
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Title | N-terminal domain of the CI repressor from bacteriophage TP901-1 | ||||||
Components | CI | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS PHAGE TP901-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Frandsen, K.H. / Rasmussen, K.K. / Poulsen, J.N. / Lo Leggio, L. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Binding of the N-Terminal Domain of the Lactococcal Bacteriophage Tp901-1 Ci Repressor to its Target DNA: A Crystallography, Small Angle Scattering, and Nuclear Magnetic Resonance Study. Authors: Frandsen, K.H. / Rasmussen, K.K. / Jensen, M.R. / Hammer, K. / Pedersen, M. / Poulsen, J.N. / Arleth, L. / Lo Leggio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zhi.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhi.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 3zhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zhi_validation.pdf.gz | 412.8 KB | Display | wwPDB validaton report |
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Full document | 3zhi_full_validation.pdf.gz | 412.8 KB | Display | |
Data in XML | 3zhi_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 3zhi_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhi ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhi | HTTPS FTP |
-Related 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: 9526.084 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 2-74 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS PHAGE TP901-1 (virus) / Cell: LACTOCOCCUS LACTIS / Plasmid: PQE-70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O48503 |
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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: 2.42 Å3/Da / Density % sol: 49.23 % / Description: NONE |
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Crystal grow | Details: 1.1M SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→18.6 Å / Num. obs: 12874 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 20.35 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.49 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→18.609 Å / SU ML: 0.11 / σ(F): 2.01 / Phase error: 19.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→18.609 Å
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Refine LS restraints |
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LS refinement shell |
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