+Open data
-Basic information
Entry | Database: PDB / ID: 6geu | ||||||
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Title | Crystal structure of the C230A mutant of human IBA57 | ||||||
Components | Putative transferase CAF17, mitochondrial | ||||||
Keywords | PROTEIN BINDING / Mitochondrial protein / Fe-S protein biogenesis / infantile leukodystrophy | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups / iron-sulfur cluster assembly / heme biosynthetic process / transferase activity / mitochondrial matrix / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Calderone, V. / Ciofi-Baffoni, S. / Gourdoupis, S. / Banci, L. / Nasta, V. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2018 Title: IBA57 Recruits ISCA2 to Form a [2Fe-2S] Cluster-Mediated Complex. Authors: Gourdoupis, S. / Nasta, V. / Calderone, V. / Ciofi-Baffoni, S. / Banci, L. #1: Journal: Acta Cryst Sect D / Year: 2019 Title: In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity. Authors: Gourdoupis, S. / Nasta, V. / Calderone, V. / Cofi-Baffoni, S. / Banci, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6geu.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6geu.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 6geu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6geu_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
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Full document | 6geu_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 6geu_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 6geu_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/6geu ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6geu | HTTPS FTP |
-Related structure data
Related structure data | 6esr 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: 33767.781 Da / Num. of mol.: 1 / Mutation: C230A Source method: isolated from a genetically manipulated source Details: The electron density is very weak or not present at all for the following residues which have been modelled automatically: 54-59, 88-92, 117, 139-143, 174-176, 299-300, 307-311, 325-327. Source: (gene. exp.) Homo sapiens (human) / Gene: IBA57, C1orf69 / Production host: Escherichia coli (E. coli) References: UniProt: Q5T440, Transferases; Transferring one-carbon groups |
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#2: 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: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35.69 Å / Num. obs: 49014 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Num. unique obs: 7712 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ESR 6esr Resolution: 1.55→35.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.422 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.082 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.846 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→35.69 Å
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Refine LS restraints |
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