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Yorodumi- PDB-4n5x: Crystal structure of N-terminal calmodulin-like Calcium sensor of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n5x | ||||||
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Title | Crystal structure of N-terminal calmodulin-like Calcium sensor of human mitochondrial ATP-Mg/Pi carrier SCaMC1 | ||||||
Components | Calcium-binding mitochondrial carrier protein SCaMC-1 | ||||||
Keywords | CALCIUM-BINDING PROTEIN / Calmodulin / Calcium sensor / mitochondrial inner membrane | ||||||
Function / homology | Function and homology information adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP transport / mitochondrial ATP transmembrane transport / ATP transmembrane transporter activity / ATP transport / mitochondrial transport / cellular response to calcium ion ...adenine nucleotide transmembrane transporter activity / adenine nucleotide transport / ATP:phosphate antiporter activity / ADP:phosphate antiporter activity / ADP transport / mitochondrial ATP transmembrane transport / ATP transmembrane transporter activity / ATP transport / mitochondrial transport / cellular response to calcium ion / cellular response to oxidative stress / mitochondrial inner membrane / calcium ion binding / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yang, Q. / Bruschweiler, S. / Chou, J. | ||||||
Citation | Journal: Structure / Year: 2014 Title: A Self-Sequestered Calmodulin-like Ca(2+) Sensor of Mitochondrial SCaMC Carrier and Its Implication to Ca(2+)-Dependent ATP-Mg/Pi Transport. Authors: Yang, Q. / Bruschweiler, S. / Chou, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n5x.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n5x.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n5x_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 4n5x_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 4n5x_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4n5x_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5x ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5x | HTTPS FTP |
-Related structure data
Related structure data | 1cllS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22932.492 Da / Num. of mol.: 1 / Fragment: UNP residues 1-193 / Mutation: C15S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC25A24, APC1, MCSC1, SCAMC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NUK1 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 100 mM CHES (pH 9.1) and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2012 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Xenocs mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→20 Å / Num. all: 10500 / Num. obs: 10443 / % possible obs: 99.73 % / Observed criterion σ(I): 2 | ||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CLL Resolution: 2.1→19.072 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.072 Å
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Refine LS restraints |
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LS refinement shell |
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