+Open data
-Basic information
Entry | Database: PDB / ID: 5j4r | ||||||
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Title | WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND 2-OXOGLUTARATE | ||||||
Components | WelO5 | ||||||
Keywords | HYDROLASE / 2-oxoglutarate and iron dependendent halogenase / small molecule halogenase | ||||||
Function / homology | 2-OXOGLUTARIC ACID / NICKEL (II) ION / WelO5 Function and homology information | ||||||
Biological species | Hapalosiphon welwitschii UTEX B 1830 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | McDonough, M.A. / Gallimore, E. / Clifton, I.J. / Schofield, C.J. | ||||||
Citation | Journal: To Be Published Title: WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND 2-OXOGLUTARATE Authors: Gallimore, E. / McDonough, M.A. / Clifton, I.J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j4r.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4r.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 5j4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4r ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4r | HTTPS FTP |
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-Related 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: 32557.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hapalosiphon welwitschii UTEX B 1830 (bacteria) Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067YX61 |
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#2: Chemical | ChemComp-AKG / |
#3: Chemical | ChemComp-NI / |
#4: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1 part Well solution: 100mM 2-(N-morpholino)ethanesulfonic acid pH 5.5, 100 mM sodium chloride, 22% polyethylene glycol 6000 added to 1 part protein 27 mg/mL, 5 mM nickel chloride, 5 mM 2- ...Details: 1 part Well solution: 100mM 2-(N-morpholino)ethanesulfonic acid pH 5.5, 100 mM sodium chloride, 22% polyethylene glycol 6000 added to 1 part protein 27 mg/mL, 5 mM nickel chloride, 5 mM 2-oxoglutarate, 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 5mM (6aS,9S,10aS)-6,6,9-trimethyl-9-vinyl-6a,7,8,10a-tetrahydro-5H-indeno[2,1-b]indol-10-one |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→47.98 Å / Num. obs: 83245 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.5 / % possible all: 51.3 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→47.976 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→47.976 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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