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- PDB-6fxj: Structure of coproheme decarboxylase from Listeria monocytogenes ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fxj | ||||||
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Title | Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III | ||||||
![]() | Putative heme-dependent peroxidase lmo2113 | ||||||
![]() | OXIDOREDUCTASE / coproheme binding / coproheme decarboxylase / pentamer | ||||||
Function / homology | ![]() hydrogen peroxide-dependent heme synthase / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hofbauer, S. / Pfanzagl, V. / Mlynek, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Authors: Milazzo, L. / Gabler, T. / Puhringer, D. / Jandova, Z. / Maresch, D. / Michlits, H. / Pfanzagl, V. / Djinovic-Carugo, K. / Oostenbrink, C. / Furtmuller, P.G. / Obinger, C. / Smulevich, G. / Hofbauer, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 907.6 KB | Display | ![]() |
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PDB format | ![]() | 631.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 60.5 KB | Display | |
Data in CIF | ![]() | 85.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fxqC ![]() 5loqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 28882.723 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lmo2113 Production host: ![]() ![]() References: UniProt: Q8Y5F1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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-Non-polymers , 5 types, 1123 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/FEC.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FEC.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-FEC / #4: Chemical | ChemComp-POL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5 20 %(w/v) PEG 4000 10 % (v/v) 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→48.8903165232 Å / Num. obs: 134739 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.083 / Rrim(I) all: 0.159 / Net I/σ(I): 6.98 |
Reflection shell | Resolution: 1.79→1.85 Å / Rmerge(I) obs: 1.147 / Rpim(I) all: 0.708 / Rrim(I) all: 1.351 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LOQ Resolution: 1.79→48.8903165232 Å / SU ML: 0.239057785055 / Cross valid method: FREE R-VALUE / σ(F): 1.3369955031 / Phase error: 26.1144393289
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8545003487 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→48.8903165232 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.64585622529 Å / Origin y: 22.4026104877 Å / Origin z: 98.3199789043 Å
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Refinement TLS group | Selection details: all |