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Open data
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Basic information
Entry | Database: PDB / ID: 4ckm | ||||||
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Title | Structure of the N-terminal domain of Leishmania SAS-6 | ||||||
![]() | SAS-6 | ||||||
![]() | STRUCTURAL PROTEIN / BASAL BODY / CENTRIOLE / CARTWHEEL / TRYPANOSOMATIDS | ||||||
Function / homology | ![]() centriole replication / centriole / ciliary basal body / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Breugel, M. | ||||||
![]() | ![]() Title: Structure of the SAS-6 cartwheel hub from Leishmania major. Authors: van Breugel, M. / Wilcken, R. / McLaughlin, S.H. / Rutherford, T.J. / Johnson, C.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 458.8 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19680.324 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 97-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % Description: STRUCTURE WAS SOLVED BY MAD USING A DATASET OBTAINED FROM CRYSTALS OF THE SELENOMETHIONINE DERIVATIVE. |
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Crystal grow | pH: 5.1 Details: 100 MM BISTRIS PH 5.1, 200 MM MGCL2, 20% (W/V) PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.86 Å / Num. obs: 48008 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 5.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.15→79.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.924 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.513 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→79.49 Å
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Refine LS restraints |
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