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Open data
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Basic information
Entry | Database: PDB / ID: 1tk1 | ||||||
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Title | YEAST OXYGEN-DEPENDENT COPROPORPHYRINOGEN OXIDASE | ||||||
![]() | Coproporphyrinogen III oxidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Phillips, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P. | ||||||
![]() | ![]() Title: Crystal Structure of the Oxygen-dependant Coproporphyrinogen Oxidase (Hem13p) of Saccharomyces cerevisiae Authors: Phillips, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 29935.641 Da / Num. of mol.: 1 / Fragment: truncated odCPO Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HEM13, YDR044W, YD5112.02 / Plasmid: pET16B / Production host: ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 50 % |
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Crystal grow![]() | Temperature: 294 K / pH: 7.5 Details: 20% PEG 3000, 0.1 M HEPES, 0.2 M sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→59.76 Å / Num. obs: 21772 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 28.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 29.6 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 7 / Rsym value: 0.585 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure![]() Resolution: 1.9→59.76 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.86 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.484 Å2
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Refine analyze | Luzzati coordinate error free: 0.144 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→59.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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