[English] 日本語
Yorodumi- PDB-2qd3: Wild type human ferrochelatase crystallized with ammonium sulfate -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qd3 | ||||||
---|---|---|---|---|---|---|---|
Title | Wild type human ferrochelatase crystallized with ammonium sulfate | ||||||
Components | Ferrochelatase | ||||||
Keywords | LYASE / Heme synthesis / Ferrochelatase / Protoporphyrin IX | ||||||
Function / homology | Function and homology information 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 / 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 | 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 | 2qd3.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qd3.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qd3 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qd3 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41178.387 Da / Num. of mol.: 2 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, 436 molecules
#2: Chemical | #3: Chemical | ChemComp-CHD / #4: Chemical | ChemComp-HEM / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05M ammonium sulfate, 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 |
Radiation | Monochromator: 1 / 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: 89810 / Num. obs: 89803 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.06 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.3 / Num. unique all: 14220 / Rsym value: 0.25 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2772860.41 / 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: 37.6198 Å2 / ksol: 0.352366 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.8 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|