+Open data
-Basic information
Entry | Database: PDB / ID: 8zkc | ||||||
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Title | iron-sulfur cluster transfer protein ApbC | ||||||
Components | Iron-sulfur cluster carrier protein | ||||||
Keywords | CYTOSOLIC PROTEIN / Iron-sulfur clusters / dimerization / disulfide bonds | ||||||
Function / homology | Function and homology information ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / mitochondrial respiratory chain complex I assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Yang, J. / Liu, L. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: Crystal structure of the iron-sulfur cluster transfer protein ApbC from Escherichia coli. Authors: Yang, J. / Duan, Y.F. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zkc.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zkc.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 8zkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zkc_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 8zkc_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 8zkc_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 8zkc_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/8zkc ftp://data.pdbj.org/pub/pdb/validation_reports/zk/8zkc | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44206.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mrp, b2113, JW2100 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AF08 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: tri-potassium citrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→55.51 Å / Num. obs: 11707 / % possible obs: 99.9 % / Redundancy: 24.3 % / CC1/2: 1 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.026 / Rrim(I) all: 0.129 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.85→2.91 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 845 / CC1/2: 0.507 / Rpim(I) all: 0.706 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→55.51 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.48 / 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: 2.85→55.51 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.1621 Å / Origin y: 40.5851 Å / Origin z: 18.7716 Å
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Refinement TLS group | Selection details: all |