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Yorodumi- PDB-1id2: CRYSTAL STRUCTURE OF AMICYANIN FROM PARACOCCUS VERSUTUS (THIOBACI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1id2 | ||||||
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Title | CRYSTAL STRUCTURE OF AMICYANIN FROM PARACOCCUS VERSUTUS (THIOBACILLUS VERSUTUS) | ||||||
Components | AMICYANIN | ||||||
Keywords | ELECTRON TRANSPORT / Beta Barrel / type-1 blue copper protein / electron transfer protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paracoccus versutus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Romero, A. / Nar, H. / Messerschmidt, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Crystal structure analysis and refinement at 2.15 A resolution of amicyanin, a type I blue copper protein, from Thiobacillus versutus. Authors: Romero, A. / Nar, H. / Huber, R. / Messerschmidt, A. / Kalverda, A.P. / Canters, G.W. / Durley, R. / Mathews, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1id2.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1id2.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1id2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1id2 ftp://data.pdbj.org/pub/pdb/validation_reports/id/1id2 | HTTPS FTP |
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-Related structure data
Related structure data | 1aanS S: Starting model for refinement |
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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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Details | The three independent molecules of amicyanin are arranged as columns around 3(2) axes centered at (0, 0) molecule C, (1/3, 2/3) molecule B and (2/3, 1/3) molecule A. The following transformation relate molecule A to B. (-0.975 -0.205 0.081) 49.109 (-0.208 0.977 -0.044) 33.553 (-0.070 -0.060 -0.996) -13.650 A to C: (0.240 -0.970 0.033) 14.988 (-0.969 -0.238 0.052) 49.233 -0.043 -0.044 -0.998) -16.988 C to B: (-0.034 0.999 -0.028) -0.062 (-0.999 -0.034 0.012) 50.335 (0.011 0.028 0.999) 1.745 |
-Components
#1: Protein | Mass: 11703.384 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus versutus (bacteria) / Gene: MAUC OR AMI / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P22365 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Reservoir: 2.05 M ammonium sulfate, 0.1 M Na, K phosphate; hanging drop: 5 microliter protein solution (6 mg/ ml) plus 4 microliter 10% (v/v) of MPD and 1.5 microliter 0.5% (v/v) beta-D- ...Details: Reservoir: 2.05 M ammonium sulfate, 0.1 M Na, K phosphate; hanging drop: 5 microliter protein solution (6 mg/ ml) plus 4 microliter 10% (v/v) of MPD and 1.5 microliter 0.5% (v/v) beta-D-glucopyranoside, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 5 / PH range high: 4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1993 / Details: Ni-filter |
Radiation | Monochromator: Ni-Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25 Å / Num. all: 92670 / Num. obs: 84144 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.073 / Rsym value: 0.079 |
Reflection shell | Resolution: 2.15→2.3 Å / Rmerge(I) obs: 0.345 / Rsym value: 0.383 / % possible all: 72.7 |
Reflection | *PLUS Num. obs: 16083 / Num. measured all: 84144 |
Reflection shell | *PLUS % possible obs: 72.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1AAN, these coordinates were supplied by the authors of this entry prior to their release Resolution: 2.15→8 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.6 Å2 | |||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Rfactor Rwork: 0.256 | |||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refine LS restraints | *PLUS
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