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Yorodumi- PDB-2h1w: Crystal structure of the His183Ala mutant variant of Bacillus sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h1w | ||||||
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Title | Crystal structure of the His183Ala mutant variant of Bacillus subtilis 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hansson, M.D. / Karlberg, T. / Arys Rahardja, M. / Al-Karadaghi, S. / Hansson, M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Amino Acid Residues His183 and Glu264 in Bacillus subtilis Ferrochelatase Direct and Facilitate the Insertion of Metal Ion into Protoporphyrin IX Authors: Hansson, M.D. / Karlberg, T. / Rahardja, M.A. / Al-Karadaghi, S. / Hansson, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1w.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1w.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2h1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1w ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1w | HTTPS FTP |
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-Related structure data
Related structure data | 2h1vC 2hk6C 1dozS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 35322.637 Da / Num. of mol.: 1 / Mutation: H183A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hemH, hemF / Plasmid: pH183A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32396, protoporphyrin ferrochelatase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-MG / |
#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: 1.97 Å3/Da / Density % sol: 37.4 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 7.4 Details: 25-30 % PEG2000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 2005 |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.3 Å / Num. all: 16655 / Num. obs: 16593 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.3 Å2 |
Reflection shell | Resolution: 2.6→2.74 Å / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DOZ Resolution: 2.6→19.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 563029.62 / 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: 32.4704 Å2 / ksol: 0.360463 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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