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Yorodumi- PDB-8t7w: Crystal structure of Oxygen-dependent coproporphyrinogen-III oxid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t7w | |||||||||
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Title | Crystal structure of Oxygen-dependent coproporphyrinogen-III oxidase (hemF) from Klebsiella aerogenes | |||||||||
Components | Oxygen-dependent coproporphyrinogen-III oxidase | |||||||||
Keywords | OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Oxygen-dependent coproporphyrinogen-III oxidase / hemF | |||||||||
Function / homology | Function and homology information coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / protein homodimerization activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Klebsiella aerogenes KCTC 2190 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of Oxygen-dependent coproporphyrinogen-III oxidase (hemF) from Klebsiella aerogenes Authors: Lovell, S. / Liu, L. / Cooper, A. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t7w.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t7w.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 8t7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/8t7w ftp://data.pdbj.org/pub/pdb/validation_reports/t7/8t7w | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35323.621 Da / Num. of mol.: 1 / Mutation: D51N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: hemF / Plasmid: KlaeA.17085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3H2C8 | ||||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus E2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene ...Details: Morpheus E2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. KlaeA.17085.a.B1.PW39170 at 43.4 mg/mL. plate 13138 well E2 drop 1. Puck: PSL-0704, Cryo: Direct. Large disorder/conformational change from H66-S85 modeled in two conformations. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 20, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.85 Å / Num. obs: 51531 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Χ2: 0.99 / Net I/σ(I): 15.8 / Num. measured all: 702985 |
Reflection shell | Resolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.453 / Num. measured all: 31620 / Num. unique obs: 2503 / CC1/2: 0.862 / Rpim(I) all: 0.424 / Rrim(I) all: 1.515 / Χ2: 0.97 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→26.15 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 22.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→26.15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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