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- PDB-5d67: Crystal structure of an EF-Hand calcium binding domain of CAP-Bin... -
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Basic information
Entry | Database: PDB / ID: 5d67 | ||||||
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Title | Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution | ||||||
![]() | EF-hand calcium-binding domain-containing protein 6 | ||||||
![]() | METAL BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Nuclear Receptor Signaling Code Biology / NHRS | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology / Partnership for Nuclear Receptor Signaling Code Biology (NHRS) | ||||||
![]() | ![]() Title: Crystal structure of an EF-Hand calcium binding domain of CAP-Binding Protein Complex-Interacting Protein 1 (EFCAB6) from Homo sapiens at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Nuclear Receptor Signaling Code Biology | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.7 KB | Display | ![]() |
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PDB format | ![]() | 133.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 454.8 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11778.729 Da / Num. of mol.: 4 / Fragment: UNP residues 1160-1260 / Mutation: D1218G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% polyethylene glycol 4000, 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 8, 2015 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→27.118 Å / Num. obs: 26723 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.787 % / Biso Wilson estimate: 26.457 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.13 / Net I/σ(I): 10.59 / Num. measured all: 197737 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
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Displacement parameters | Biso max: 161.22 Å2 / Biso mean: 35.3461 Å2 / Biso min: 10.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.209 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.118 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Total num. of bins used: 13
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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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