+Open data
-Basic information
Entry | Database: PDB / ID: 4f4d | ||||||
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Title | F337R variant of human ferrochelatase | ||||||
Components | Ferrochelatase, mitochondrial | ||||||
Keywords | LYASE / FERROCHELATASE / HEME BIOSYNTHESIS | ||||||
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: 1.8 Å | ||||||
Authors | Lanzilotta, W.N. / Medlock, A.E. / Dailey, T.E. / Dailey, H.A. | ||||||
Citation | Journal: TO BE PUBLISHED Title: F337R Variant of Human Ferrochelatase Authors: Lanzilotta, W.N. / Medlock, A.E. / Dailey, T.E. / Dailey, H.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f4d.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4d.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 4f4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4d ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4d | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 41188.410 Da / Num. of mol.: 2 / Fragment: unp residues 65-423 / Mutation: F337R 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 |
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-Non-polymers , 5 types, 615 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-CHD / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % |
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Crystal grow | pH: 6.5 Details: 0.1 M BIS-TRIS, 0.05 M AMMONIUM ACETATE, 20% PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH) , PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 210 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2008 |
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: 1.8→50 Å / Num. obs: 165467 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Rmerge(I) obs: 0.089 / Rsym value: 0.085 / Net I/σ(I): 40.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Highest resolution: 1.8 Å / SU B: 2.218 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.72 Å2
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Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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