+Open data
-Basic information
Entry | Database: PDB / ID: 2hrc | ||||||
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Title | 1.7 angstrom structure of human ferrochelatase variant R115L | ||||||
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: 1.7 Å | ||||||
Authors | Medlock, A. / Swartz, L. / Dailey, T.A. / Dailey, H.A. / Lanzilotta, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Substrate interactions with human ferrochelatase Authors: Medlock, A. / Swartz, L. / Dailey, T.A. / Dailey, H.A. / Lanzilotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrc.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrc.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrc ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrc | HTTPS FTP |
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-Related structure data
Related structure data | 2hreC 1hrkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41134.348 Da / Num. of mol.: 2 / Mutation: R115L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: jm109 / Gene: FECH / Plasmid: pTRCHis / Production host: Escherichia coli (E. coli) / References: UniProt: P22830, protoporphyrin ferrochelatase |
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-Non-polymers , 6 types, 617 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CHD / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M calcium chloride, 0.1 M Bis-Tris, 30% v/v PEG MME 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2005 |
Radiation | Monochromator: 0.98 angstroms / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 100689 / Num. obs: 100275 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.071 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.147 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HRK Resolution: 1.7→41.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1948100.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5561 Å2 / ksol: 0.369932 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→41.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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