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- PDB-5wgb: Crystal Structure of the Human mitochondrial Cysteine Desulfurase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wgb | ||||||
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Title | Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and E. coli ACP1 protein at 2.75A | ||||||
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![]() | TRANSFERASE / Human mitochondrial cysteine desulfurse LYR Motif containing protein 4 Acyl Carrier Protein 1 (E.coli) | ||||||
Function / homology | ![]() molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process ...molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial [2Fe-2S] assembly complex / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / lipid A biosynthetic process / iron-sulfur cluster binding / acyl binding / acyl carrier activity / pyridoxal phosphate binding / nuclear body / mitochondrial matrix / centrosome / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boniecki, M.T. / Cygler, M. | ||||||
![]() | ![]() Title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Authors: Boniecki, M.T. / Freibert, S.A. / Muhlenhoff, U. / Lill, R. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.1 KB | Display | ![]() |
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PDB format | ![]() | 146.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 631.5 KB | Display | ![]() |
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Full document | ![]() | 636.6 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wkpC ![]() 5wlwC ![]() 3lvmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47395.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10763.483 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 8514.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S88 / ExPEC / Gene: acpP, ECS88_1108 / Production host: ![]() ![]() |
#4: Chemical | ChemComp-PLP / |
#5: Chemical | ChemComp-8Q1 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.65 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5 0.3 M Ammonium Acetate 20 mM Calcium Acetate 20 mM CaCl2 19 % isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→32.1 Å / Num. obs: 20346 / % possible obs: 99.59 % / Redundancy: 10.9 % / CC1/2: 0.998 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 11.3 % / Num. unique obs: 2020 / CC1/2: 0.788 / % possible all: 99.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LVM Resolution: 2.75→32.1 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.17 / 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: 2.75→32.1 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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