+Open data
-Basic information
Entry | Database: PDB / ID: 1hrk | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN FERROCHELATASE | ||||||
Components | FERROCHELATASE | ||||||
Keywords | LYASE / ferrochelatase / Fe2S2 Cluster / heme biosynthesis / PROTOHEME FERRO-LYASE / mature length / proteolytically processed mitochondrial inner membrane protein | ||||||
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 / generation of precursor metabolites and energy / cellular response to dexamethasone stimulus / cholesterol metabolic process / erythrocyte differentiation / Mitochondrial protein degradation / 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 / SAD / Resolution: 2 Å | ||||||
Authors | Wu, C.K. / Dailey, H.A. / Rose, J.P. / Burden, A. / Sellers, V.M. / Wang, B.-C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis. Authors: Wu, C.K. / Dailey, H.A. / Rose, J.P. / Burden, A. / Sellers, V.M. / Wang, B.C. #1: Journal: Biochim.Biophys.Acta / Year: 1999 Title: Human Ferrochelatase: crystallization, characterization of the [2Fe-2S] cluster and determination that the enzyme is a homodimer Authors: Burden, A.E. / Wu, C.-K. / Dailey, T.A. / Busch, J.L.H. / Dhawan, I.K. / Rose, J.P. / Wang, B.C. / 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 | 1hrk.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hrk.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hrk_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1hrk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1hrk_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1hrk_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/1hrk ftp://data.pdbj.org/pub/pdb/validation_reports/hr/1hrk | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 41134.348 Da / Num. of mol.: 2 / Fragment: MATURE LENGTH / Mutation: R115L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHDTF20 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22830, protoporphyrin ferrochelatase #2: Chemical | ChemComp-CHD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, ammonium sulfate, sodium phosphate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃Details: Burden, A.E., (1999) Biochim.Biophys.Acta, 1435, 191. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | ||||||||||||||||||
Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 60384 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Redundancy: 20 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 48 | ||||||||||||||||||
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 10 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 12 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2442692.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.61 Å2 / ksol: 0.3843 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 3.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.243 / % reflection Rfree: 3 % / Rfactor Rwork: 0.209 |