+Open data
-Basic information
Entry | Database: PDB / ID: 1doz | ||||||
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Title | CRYSTAL STRUCTURE OF FERROCHELATASE | ||||||
Components | FERROCHELATASE | ||||||
Keywords | LYASE / ROSSMANN FOLD / PI-HELIX | ||||||
Function / homology | Function and homology information coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Lecerof, D. / Fodje, M. / Hansson, A. / Hansson, M. / Al-Karadaghi, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structural and mechanistic basis of porphyrin metallation by ferrochelatase. Authors: Lecerof, D. / Fodje, M. / Hansson, A. / Hansson, M. / Al-Karadaghi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1doz.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1doz.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1doz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1doz_validation.pdf.gz | 418.4 KB | Display | wwPDB validaton report |
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Full document | 1doz_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 1doz_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1doz_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1doz ftp://data.pdbj.org/pub/pdb/validation_reports/do/1doz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35258.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P32396, protoporphyrin ferrochelatase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.95 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG2000, MAGNESIUM CHLORIDE, TRIS, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Details: used to microseeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→19.95 Å / Num. obs: 27034 / % possible obs: 97.8 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.22 / % possible all: 98.4 |
Reflection shell | *PLUS % possible obs: 98.4 % |
-Processing
Software |
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Refinement | Resolution: 1.8→14.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1469610.4 / 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: 41.34 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.177 / Rfactor Rfree: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.208 |