+Open data
-Basic information
Entry | Database: PDB / ID: 4kmm | ||||||
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Title | M76H variant of human ferrochelatase | ||||||
Components | Ferrochelatase, mitochondrial | ||||||
Keywords | LYASE / metal chelatase / mitochondria | ||||||
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: 2.6 Å | ||||||
Authors | Lanzilotta, W.N. / Medlock, A.E. | ||||||
Citation | Journal: To be Published Title: M76H variant of human ferrochelatase Authors: Lanzilotta, W.N. / Medlock, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kmm.cif.gz | 161.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kmm.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/4kmm ftp://data.pdbj.org/pub/pdb/validation_reports/km/4kmm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit represents the relevant biological assembly. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42403.645 Da / Num. of mol.: 2 / Mutation: M76H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FECH / References: UniProt: P22830, protoporphyrin ferrochelatase |
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-Non-polymers , 5 types, 119 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CHD / #5: Chemical | #6: 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: 2.75 Å3/Da / Density % sol: 55.34 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→71.26 Å / Num. all: 28630 / Num. obs: 26185 / % possible obs: 86.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→71.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.308 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 1.05 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.849 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→71.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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