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Yorodumi- PDB-3ox6: Crystal Structure of the calcium sensor calcium-binding protein 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ox6 | ||||||
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Title | Crystal Structure of the calcium sensor calcium-binding protein 1 (CaBP1) | ||||||
Components | Calcium-binding protein 1 | ||||||
Keywords | calcium binding protein / EF-hand / Calcium-sensor / calcium binding | ||||||
Function / homology | Function and homology information enzyme inhibitor activity / response to stimulus / Sensory processing of sound by inner hair cells of the cochlea / nuclear localization sequence binding / negative regulation of protein import into nucleus / calcium channel regulator activity / visual perception / calcium-dependent protein binding / cell cortex / postsynaptic density ...enzyme inhibitor activity / response to stimulus / Sensory processing of sound by inner hair cells of the cochlea / nuclear localization sequence binding / negative regulation of protein import into nucleus / calcium channel regulator activity / visual perception / calcium-dependent protein binding / cell cortex / postsynaptic density / cytoskeleton / Golgi membrane / calcium ion binding / perinuclear region of cytoplasm / extracellular space / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Findeisen, F. / Minor, D.L. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structural Basis for the Differential Effects of CaBP1 and Calmodulin on Ca(V)1.2 Calcium-Dependent Inactivation. Authors: Findeisen, F. / Minor, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ox6.cif.gz | 369.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ox6.ent.gz | 305 KB | Display | PDB format |
PDBx/mmJSON format | 3ox6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/3ox6 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3ox6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 17764.975 Da / Num. of mol.: 6 / Fragment: UNP residues 219-370 / Mutation: K130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CABP1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q9NZU7 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-HEZ / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.9M (NH4)2SO4, 5-7% 1,6-hexanediol, 0.1M citrate/sodium citrate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97958, 0.97972, 1.01987 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2008 | ||||||||||||
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 38309 / Num. obs: 38103 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.072 / Net I/σ(I): 7.1 | ||||||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.432 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.901 / SU B: 27.78 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.579 / ESU R Free: 0.319 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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