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- PDB-3lb5: Crystal structure of Hit-like protein involved in cell-cycle regu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lb5 | ||||||
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Title | Crystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand | ||||||
![]() | Hit-like protein involved in cell-cycle regulation | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 94.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3imiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 18102.795 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | ![]() Compound details | THE COORDINATES OF LIGAND UNL RESEMBLES NICOTINAMIDE. BUT NICOTINAMIDE WAS NOT ADDED TO THE SAMPLE. ...THE COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR ...Details: PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→20 Å / Num. obs: 75981 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 26.426 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.36 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 15334 / Num. unique all: 5338 / Num. unique obs: 5338 / % possible all: 94.4 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 57.16 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3imi Resolution: 1.9→19.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.868 / SU B: 7.654 / SU ML: 0.103 / SU R Cruickshank DPI: 0.17 / SU Rfree: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.97 Å2 / Biso mean: 12.896 Å2 / Biso min: 2.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 971 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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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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