+Open data
-Basic information
Entry | Database: PDB / ID: 1ak1 | ||||||
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Title | FERROCHELATASE FROM BACILLUS SUBTILIS | ||||||
Components | FERROCHELATASE | ||||||
Keywords | PROTOHEME FERRO-LYASE / HEME SYNTHESIS / PORPHYRIN / METALLATION / B. SUBTILIS | ||||||
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 / MIR / Resolution: 1.9 Å | ||||||
Authors | Al-Karadaghi, S. / Hansson, M. / Nikonov, S. / Jonsson, B. / Hederstedt, L. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Crystal structure of ferrochelatase: the terminal enzyme in heme biosynthesis. Authors: Al-Karadaghi, S. / Hansson, M. / Nikonov, S. / Jonsson, B. / Hederstedt, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ak1.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ak1.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ak1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ak1_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 1ak1_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1ak1_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1ak1_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1ak1 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1ak1 | 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: 35389.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: HEMH / Organ: SEED / Plasmid: BL21 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HEMH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P32396, protoporphyrin ferrochelatase |
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#2: 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: 2.1 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: seeded / pH: 8.5 Details: CRYSTALS GROW IN 30% PEG 2000, 0.2 M MGCL2 0.1 M TRIS-HCL, PH 8.5. THESE WERE VORTEXED AND USED AS SEEDS FOR LARGE SINGLE CRYSTALS IN: 27% PEG 2000, 0.2 M MGCL2, 0.05% NAN3, 0.1 M TRIS-HCL, PH 8.5, seeded | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.859 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1995 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.859 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 24332 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.44 / % possible all: 80 |
Reflection | *PLUS Num. measured all: 226242 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 80.1 % / Rmerge(I) obs: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→10 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 21258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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