[English] 日本語
Yorodumi- PDB-3zhm: N-terminal domain of the CI repressor from bacteriophage TP901-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zhm | ||||||
---|---|---|---|---|---|---|---|
Title | N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS PHAGE TP901-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zhm.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zhm.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zhm_validation.pdf.gz | 406.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3zhm_full_validation.pdf.gz | 406.1 KB | Display | |
Data in XML | 3zhm_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 3zhm_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhm ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhm | HTTPS FTP |
-Related structure data
Related structure data | 3zhiC 2r1jS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9105.513 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-74 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS PHAGE TP901-1 (virus) / Plasmid: PQE-70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O48503 |
---|---|
#2: DNA chain | Mass: 5515.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) LACTOCOCCUS PHAGE TP901-1 (virus) |
#3: DNA chain | Mass: 5515.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) LACTOCOCCUS PHAGE TP901-1 (virus) |
#4: Water | ChemComp-HOH / |
Sequence details | OLIGONUCLE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.45 % / Description: NONE |
---|---|
Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→33.91 Å / Num. obs: 4365 / % possible obs: 100 % / Observed criterion σ(I): 1.36 / Redundancy: 4.4 % / Biso Wilson estimate: 22.41 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R1J Resolution: 2.6→33.91 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 17.9 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→33.91 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|