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- PDB-2qd1: 2.2 Angstrom Structure of the human ferrochelatase variant E343K ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qd1 | ||||||
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Title | 2.2 Angstrom Structure of the human ferrochelatase variant E343K with substrate bound | ||||||
![]() | Ferrochelatase | ||||||
![]() | LYASE / Ferrochelatase / heme biosynthesis / protopophyrin IX | ||||||
Function / homology | ![]() protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / regulation of eIF2 alpha phosphorylation by heme / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / heme B biosynthetic process / heme O biosynthetic process ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / regulation of eIF2 alpha phosphorylation by heme / detection of UV / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / heme B biosynthetic process / heme O biosynthetic process / ferrochelatase activity / heme A biosynthetic process / very-low-density lipoprotein particle assembly / response to methylmercury / response to arsenic-containing substance / Heme biosynthesis / heme biosynthetic process / response to light stimulus / Mitochondrial protein degradation / cholesterol metabolic process / erythrocyte differentiation / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / response to lead ion / ferrous iron binding / 2 iron, 2 sulfur cluster binding / multicellular organismal-level iron ion homeostasis / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / heme binding / protein homodimerization activity / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Medlock, A.E. / Dailey, T.A. / Ross, T.A. / Dailey, H.A. / Lanzilotta, W.N. | ||||||
![]() | ![]() Title: A pi-Helix Switch Selective for Porphyrin Deprotonation and Product Release in Human Ferrochelatase. Authors: Medlock, A.E. / Dailey, T.A. / Ross, T.A. / Dailey, H.A. / Lanzilotta, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.1 KB | Display | ![]() |
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PDB format | ![]() | 260.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 67.1 KB | Display | |
Data in CIF | ![]() | 90.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41178.453 Da / Num. of mol.: 4 / Mutation: E343K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 699 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/PP9.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PP9.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FES / #3: Chemical | ChemComp-PP9 / #4: Chemical | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M ammonium acetate, 0.05M Bis-Tris, pH 6.5 and 40% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2006 |
Radiation | Monochromator: 1.0 angstroms / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 86145 / Num. obs: 82197 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.062 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.6 / Num. unique all: 15098 / Rsym value: 0.18 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7099 Å2 / ksol: 0.396886 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→42.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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