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Yorodumi- PDB-1oih: Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oih | ||||||
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Title | Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase | ||||||
Components | PUTATIVE ALKYLSULFATASE ATSK | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE / ALKYLSULFATASE / JELLY ROLL | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.89 Å | ||||||
Authors | Mueller, I. / Kahnert, A. / Pape, T. / Dierks, T. / Meyer-Klauke, W. / Kertesz, M. / Uson, I. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure of the Alkylsulfatase Atsk: Insights Into the Catalytic Mechanism of the Fe(II) -Ketoglutarate-Dependent Dioxygenase Superfamily Authors: Mueller, I. / Kahnert, A. / Pape, T. / Sheldrick, G.M. / Meyer-Klaucke, W. / Dierks, T. / Kertesz, M. / Uson, I. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oih.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oih.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oih ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oih | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 33248.402 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5 #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 25 MM NA ACETATE, 25 MM NA CITRATE PH 5.6, 7% PEG 4000, 30% GLYCEROL | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8439 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→20 Å / Num. obs: 134420 / % possible obs: 99.6 % / Redundancy: 5.34 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.21 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.3566 / Mean I/σ(I) obs: 4.32 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 20 Å / Num. measured all: 719684 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.32 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.257 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
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