[English] 日本語
Yorodumi- PDB-2qd1: 2.2 Angstrom Structure of the human ferrochelatase variant E343K ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qd1 | ||||||
---|---|---|---|---|---|---|---|
Title | 2.2 Angstrom Structure of the human ferrochelatase variant E343K with substrate bound | ||||||
Components | Ferrochelatase | ||||||
Keywords | LYASE / Ferrochelatase / heme biosynthesis / protopophyrin IX | ||||||
Function / homology | Function and homology information protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / regulation of eIF2 alpha phosphorylation by heme / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / ferrochelatase activity / very-low-density lipoprotein particle assembly ...protoporphyrinogen IX metabolic process / regulation of hemoglobin biosynthetic process / detection of UV / regulation of eIF2 alpha phosphorylation by heme / iron-responsive element binding / response to platinum ion / protoporphyrin ferrochelatase / response to insecticide / ferrochelatase activity / very-low-density lipoprotein particle assembly / response to methylmercury / response to arsenic-containing substance / Heme biosynthesis / heme biosynthetic process / response to light stimulus / cholesterol metabolic process / cellular response to dexamethasone stimulus / erythrocyte differentiation / generation of precursor metabolites and energy / ferrous iron binding / response to lead ion / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Medlock, A.E. / Dailey, T.A. / Ross, T.A. / Dailey, H.A. / Lanzilotta, W.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qd1.cif.gz | 308.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qd1.ent.gz | 260.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qd1 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qd1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: FECH / Production host: Escherichia coli (E. coli) / References: UniProt: P22830, protoporphyrin ferrochelatase |
---|
-Non-polymers , 5 types, 699 molecules
#2: Chemical | ChemComp-FES / #3: Chemical | ChemComp-PP9 / #4: Chemical | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 133770.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7099 Å2 / ksol: 0.396886 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.08 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|