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- PDB-1kca: Crystal Structure of the lambda Repressor C-terminal Domain Octamer -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kca | ||||||
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Title | Crystal Structure of the lambda Repressor C-terminal Domain Octamer | ||||||
![]() | REPRESSOR PROTEIN CI | ||||||
![]() | GENE REGULATION / dna-binding / lambda repressor / protein oligomerization / dna-looping | ||||||
Function / homology | ![]() maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bell, C.E. / Lewis, M. | ||||||
![]() | ![]() Title: Crystal structure of the lambda repressor C-terminal domain octamer. Authors: Bell, C.E. / Lewis, M. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE GSHM (128-131) IS FROM THE EXPRESSION VECTOR (GS FROM THE THROMBIN SITE, AND ...SEQUENCE THE SEQUENCE GSHM (128-131) IS FROM THE EXPRESSION VECTOR (GS FROM THE THROMBIN SITE, AND HIS MET FROM THE NDEI SITE). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.4 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f39S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is the octamer that is in the asmmetric unit |
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Components
#1: Protein | Mass: 11849.380 Da / Num. of mol.: 8 / Fragment: C-terminal domain (residues 132-236) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.55 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium formate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→23.5 Å / Num. obs: 33013 / % possible obs: 99.2 % / Observed criterion σ(I): -2 / Redundancy: 1.6 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 4.5 |
Reflection shell | Highest resolution: 2.9 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.8 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 53445 |
Reflection shell | *PLUS % possible obs: 95 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F39 Resolution: 2.91→23.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 893314.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.0074 Å2 / ksol: 0.372394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→23.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.91→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.384 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.339 |