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Yorodumi- PDB-2r13: Crystal structure of human mitoNEET reveals a novel [2Fe-2S] clus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r13 | ||||||
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Title | Crystal structure of human mitoNEET reveals a novel [2Fe-2S] cluster coordination | ||||||
Components | Zinc finger CDGSH domain-containing protein 1 | ||||||
Keywords | METAL BINDING PROTEIN / beta-beta-alpha-beta topology / Acetylation / Metal-binding / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion ...protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Hou, X. / Liu, R. / Ross, S. / Smart, E.J. / Zhu, H. / Gong, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystallographic studies of human MitoNEET Authors: Hou, X. / Liu, R. / Ross, S. / Smart, E.J. / Zhu, H. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r13.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r13.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r13 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r13 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9220.584 Da / Num. of mol.: 1 / Fragment: cytoplasmic part, residues 30-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NZ45 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-FES / |
#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: 4.13 Å3/Da / Density % sol: 70.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 2.0M NaCl, 0.1M Tris-HCl pH5.5-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 14636 / % possible obs: 99.4 % / Redundancy: 9.1 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.975 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.44 / Num. unique all: 714 / Χ2: 1.454 / % possible all: 99 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.352 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.081 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.298 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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