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- PDB-7bji: Crystal structure of the Danio rerio centrosomal protein Cep135 c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bji | ||||||
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Title | Crystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190 | ||||||
![]() | Centrosomal protein of 135 kDa | ||||||
![]() | STRUCTURAL PROTEIN / centriole / centrosome / coiled coil / pinehead / alpha helix | ||||||
Function / homology | ![]() : / : / : / : / Anchoring of the basal body to the plasma membrane / : / Regulation of PLK1 Activity at G2/M Transition / centriole-centriole cohesion / centriole replication / centriole / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Q. / Hatzopoulos, G. / Iller, O. / Vakonakis, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190 Authors: Li, Q. / Hatzopoulos, G. / Iller, O. / Vakonakis, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.2 KB | Display | ![]() |
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PDB format | ![]() | 133.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14984.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 18 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 15 mg/ml DrCep135 64-190 in 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP; 0.2 M ammonium acetate, 0.1 M sodium acetate, 15% w/v PEG 4000, pH 4 mother liquor; 1:2 protein / mother liquor ratio, 300nl drops |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→89.97 Å / Num. obs: 28078 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 87.85 Å2 / CC1/2: 1 / Rrim(I) all: 0.091 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.58→2.62 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1392 / CC1/2: 0.5 / Rrim(I) all: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 124.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.58→63.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.6 Å / Total num. of bins used: 50
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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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