+Open data
-Basic information
Entry | Database: PDB / ID: 6odd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human complex ACP-ISD11 | ||||||
Components |
| ||||||
Keywords | BIOSYNTHETIC PROTEIN / Iron Sulfur Clusters / Cysteine desulfurase activity regulator | ||||||
Function / homology | Function and homology information [4Fe-4S] cluster assembly / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding ...[4Fe-4S] cluster assembly / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / Glyoxylate metabolism and glycine degradation / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / aerobic respiration / fatty acid binding / mitochondrial membrane / fatty acid biosynthetic process / mitochondrial inner membrane / nuclear body / mitochondrial matrix / calcium ion binding / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Herrera, M.G. / Noguera, M.E. / Klinke, S. / Santos, J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: Structure of the Human ACP-ISD11 Heterodimer. Authors: Herrera, M.G. / Noguera, M.E. / Sewell, K.E. / Agudelo Suarez, W.A. / Capece, L. / Klinke, S. / Santos, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6odd.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6odd.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 6odd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6odd_validation.pdf.gz | 631.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6odd_full_validation.pdf.gz | 631.4 KB | Display | |
Data in XML | 6odd_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6odd_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/6odd ftp://data.pdbj.org/pub/pdb/validation_reports/od/6odd | HTTPS FTP |
-Related structure data
Related structure data | 5wgbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 9845.247 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDUFAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14561 |
---|---|
#2: Protein | Mass: 8833.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34 |
#3: Chemical | ChemComp-8Q1 / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 64.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The drop was a 1:1 mix of protein (in 10 mM Tris buffer, 25 mM NaCl, pH 7.5) and reservoir solution (0.1 M Tris pH 9.1, 0.1 M CaCl2, 23% tert-butanol) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019 Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→43.553 Å / Num. obs: 21240 / % possible obs: 99.7 % / Redundancy: 39.695 % / Biso Wilson estimate: 53.192 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.078 / Χ2: 1.227 / Net I/σ(I): 32.54 / Num. measured all: 843114 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WGB Resolution: 2→43.553 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.74
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.4 Å2 / Biso mean: 66.6292 Å2 / Biso min: 40.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→43.553 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|