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Open data
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Basic information
Entry | Database: PDB / ID: 6sv3 | ||||||
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Title | Structure of coproheme-LmCpfC | ||||||
![]() | Ferrochelatase | ||||||
![]() | METAL BINDING PROTEIN / Ferrochelatase / Prokaryotic heme biosynthesis / ferredoxin-like fold | ||||||
Function / homology | ![]() coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hofbauer, S. / Helm, J. / Djinovic-Carugo, K. / Furtmueller, P.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures and calorimetry reveal catalytically relevant binding mode of coproporphyrin and coproheme in coproporphyrin ferrochelatase. Authors: Hofbauer, S. / Helm, J. / Obinger, C. / Djinovic-Carugo, K. / Furtmuller, P.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.7 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839.9 KB | Display | ![]() |
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Full document | ![]() | 845.3 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rwvC ![]() 2hk6S 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
#1: Protein | Mass: 35632.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hemH, A4G43_07995, AF115_13645, AP101_13400, AP103_13395, AP112_12715, AP127_13135, AP130_13225, APD66_13050, ARS86_05675, B1N21_11380, B4Y57_13635, B5G78_12175, B5H07_07285, BRS71_03785, D3X95_ ...Gene: hemH, A4G43_07995, AF115_13645, AP101_13400, AP103_13395, AP112_12715, AP127_13135, AP130_13225, APD66_13050, ARS86_05675, B1N21_11380, B4Y57_13635, B5G78_12175, B5H07_07285, BRS71_03785, D3X95_05200, D3Y03_05130, D8K64_06195, EAJ22_07595, EAX63_13360, EFX44_12300, SG10_07760 Production host: ![]() ![]() References: UniProt: A0A3T2BSC5, UniProt: Q8Y565*PLUS, protoporphyrin ferrochelatase | ||||
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#2: Chemical | ChemComp-FEC / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 5.5, 25% PEG3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→36.51 Å / Num. obs: 37446 / % possible obs: 99.04 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04989 / Rpim(I) all: 0.04989 / Rrim(I) all: 0.07055 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 1.64→1.699 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3635 / CC1/2: 0.561 / Rpim(I) all: 0.607 / Rrim(I) all: 0.8584 / % possible all: 96.68 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HK6 Resolution: 1.64000868883→36.5007995703 Å / SU ML: 0.300070196581 / Cross valid method: FREE R-VALUE / σ(F): 1.34351924443 / Phase error: 23.0195528204
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8354837015 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64000868883→36.5007995703 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: 0.716000931266 Å / Origin y: 2.40036501387 Å / Origin z: -11.6151507726 Å
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Refinement TLS group | Selection details: (chain A and resseq 3:311) |