+Open data
-Basic information
Entry | Database: PDB / ID: 1a7d | ||||||
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Title | CHLOROMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA | ||||||
Components | MYOHEMERYTHRIN | ||||||
Keywords | OXYGEN TRANSPORT / NONHEME IRON OXYGEN CARRIER | ||||||
Function / homology | Function and homology information inorganic ion homeostasis / monoatomic cation homeostasis / oxygen carrier activity / iron ion binding Similarity search - Function | ||||||
Biological species | Themiste zostericola (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Martins, L.J. / Hill, C.P. / Ellis Junior, W.R. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution. Authors: Martins, L.J. / Hill, C.P. / Ellis Jr., W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a7d.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a7d.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1a7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7d ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7d | 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: 13800.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CONTAINS A CHLORO-DIIRON-OXO (FE1-O-FE2) MOIETY (CFO). Source: (gene. exp.) Themiste zostericola (invertebrata) / Tissue: RETRACTOR MUSCLES / Cell line: BL21 / Plasmid: PMHR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02247 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CFO / | #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: 2.27 Å3/Da / Density % sol: 45.76 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0) | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 119 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1988 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→10 Å / Num. obs: 12376 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.076 |
Reflection | *PLUS Num. measured all: 91983 |
Reflection shell | *PLUS Highest resolution: 1.74 Å / Lowest resolution: 1.8 Å / % possible obs: 58.3 % |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 10.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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