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Yorodumi- PDB-1c9e: STRUCTURE OF FERROCHELATASE WITH COPPER(II) N-METHYLMESOPORPHYRIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c9e | ||||||
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Title | STRUCTURE OF FERROCHELATASE WITH COPPER(II) N-METHYLMESOPORPHYRIN COMPLEX BOUND AT THE ACTIVE SITE | ||||||
Components | PROTOHEME FERROLYASE | ||||||
Keywords | LYASE / BACILLUS SUBTILIS / CHELATASE / PORPHYRIN METALLATION / N-METHYLMESOPORPHYRIN / HEME SYNTHESIS | ||||||
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: 2.3 Å | ||||||
Authors | Lecerof, D. / Fodje, M.N. / 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 | 1c9e.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9e.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9e ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9e | HTTPS FTP |
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-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: 34885.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Bacteria (eubacteria) / References: UniProt: P32396, protoporphyrin ferrochelatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-MP1 / |
#4: 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: 39.97 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG 2000, magnesium chloride, TRIS, copper sulfate, N-methylmesoporphyrin, 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 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.168 Å / Num. obs: 12500 / % possible obs: 94.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.28 / % possible all: 96.6 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % possible obs: 94.2 % / Redundancy: 0 % |
Reflection shell | *PLUS % possible obs: 96.6 % |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1385645.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: USED MAXIMUM LIKELIHOOD TARGET WITH AMPLITUDES
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.31 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7.2 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.257 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.291 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.228 |