+Open data
-Basic information
Entry | Database: PDB / ID: 3ie9 | ||||||
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Title | Structure of oxidized M98L mutant of amicyanin | ||||||
Components | Amicyanin | ||||||
Keywords | ELECTRON TRANSPORT / TYPE-I BLUE COPPER PROTEIN / BETA SANDWICH / Copper / Metal-binding / Periplasm / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Sukumar, N. / Davidson, V.L. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. Authors: Choi, M. / Sukumar, N. / Liu, A. / Davidson, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ie9.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ie9.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ie9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3ie9 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3ie9 | HTTPS FTP |
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-Related structure data
Related structure data | 3ieaC 1aacS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11487.133 Da / Num. of mol.: 1 / Fragment: residues 27-131 / Mutation: M98L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ami, mauC / Plasmid: pMEG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22364 |
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-Non-polymers , 6 types, 87 molecules
#2: Chemical | ChemComp-PO4 / |
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#3: Chemical | ChemComp-CU / |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-CL / |
#6: Chemical | ChemComp-ACT / |
#7: 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: 4.39 Å3/Da / Density % sol: 71.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.3808 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3808 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 12438 / % possible obs: 99 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AAC Resolution: 2.1→50 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.86 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML Details: PO4 CONTAINS TWO OXYGEN ATOMS INSTEAD OF FOUR. IT IS LOCATED ON A TWO-FOLD AXIS AND SYMMETRY GENERATES OTHER TWO OXYGEN ATOMS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.218 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.19 Å2 / Biso mean: 37 Å2 / Biso min: 23.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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