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- PDB-5t2k: Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III -
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Open data
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Basic information
Entry | Database: PDB / ID: 5t2k | ||||||
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Title | Geobacillus stearothermophilus HemQ with Manganese-Coproporphyrin III | ||||||
![]() | Putative heme-dependent peroxidase GT50_08830 | ||||||
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Function / homology | ![]() hydrogen peroxide-dependent heme synthase / heme biosynthetic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gauss, G.H. / Celis, A.I. / Dubois, J.L. / Peters, J.W. | ||||||
![]() | ![]() Title: Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). Authors: Celis, A.I. / Gauss, G.H. / Streit, B.R. / Shisler, K. / Moraski, G.C. / Rodgers, K.R. / Lukat-Rodgers, G.S. / Peters, J.W. / DuBois, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 505.7 KB | Display | ![]() |
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PDB format | ![]() | 423.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1t0tS S: Starting model for refinement |
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Similar 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
#1: Protein | Mass: 28817.609 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GT50_08830 / Production host: ![]() ![]() ![]() References: UniProt: A0A0K2H9D8, ![]() #2: Chemical | ChemComp-76R / [ #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.05 M cadmium sulfate, 0.8-1.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→38.4 Å / Num. obs: 142652 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.824 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1T0T Resolution: 1.8→38.4 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→38.4 Å
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Refine LS restraints |
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LS refinement shell |
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