+Open data
-Basic information
Entry | Database: PDB / ID: 6rwv | ||||||
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Title | Structure of apo-LmCpfC | ||||||
Components | Ferrochelatase | ||||||
Keywords | METAL BINDING PROTEIN / Ferrochelatase / Prokaryotic heme biosynthesis / ferredoxin-like fold | ||||||
Function / homology | Function and homology information coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63863795352 Å | ||||||
Authors | Hofbauer, S. / Helm, J. / Djinovic-Carugo, K. / Furtmueller, P.G. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Febs J. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rwv.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rwv.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwv ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwv | HTTPS FTP |
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-Related structure data
Related structure data | 6sv3C 2hk6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35770.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) 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: Escherichia coli (E. coli) References: UniProt: A0A3T2BSC5, UniProt: Q8Y565*PLUS, protoporphyrin ferrochelatase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 16% w/v PEG 8000, 20% w/v Glycerol, 0.04 M KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.63863795352→50.0905681247 Å / Num. obs: 44834 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 18.060682719 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06407 / Rpim(I) all: 0.06407 / Rrim(I) all: 0.09061 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.639→1.698 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6822 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 4416 / CC1/2: 0.435 / Rpim(I) all: 0.6822 / Rrim(I) all: 0.9648 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HK6 Resolution: 1.63863795352→50.0905681247 Å / SU ML: 0.19115048118 / Cross valid method: FREE R-VALUE / σ(F): 1.33645276556 / Phase error: 21.9177428424
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3643472954 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63863795352→50.0905681247 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: 15.3388808755 Å / Origin y: 41.8680056253 Å / Origin z: 31.9168207735 Å
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Refinement TLS group | Selection details: (chain A and resseq 3:312) |