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Yorodumi- PDB-1oik: Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oik | ||||||
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Title | Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with fe, alphaketoglutarate and 2-ethyl-1-hexanesulfuric acid | ||||||
Components | PUTATIVE ALKYLSULFATASE ATSK | ||||||
Keywords | OXIDOREDUCTASE / JELLY ROLL | ||||||
Function / homology | Function and homology information alkyl sulfatase / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Mueller, I. / Kahnert, A. / Pape, T. / Dierks, T. / Meyer-Klauke, W. / Kertesz, M.A. / Uson, I. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure of the Alkylsulfatase Atsk: Insights Into the Catalytic Mechanism of the Fe(II) Alpha-Ketoglutarate-Dependent Dioxygenase Superfamily Authors: Mueller, I. / Kahnert, A. / Pape, T. / Sheldrick, G.M. / Meyer-Klaucke, W. / Dierks, T. / Kertesz, M.A. / Uson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oik.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oik.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oik_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 1oik_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 1oik_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1oik_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oik ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oik | HTTPS FTP |
-Related structure data
Related structure data | 1oihSC 1oiiC 1oijC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-1, 0.016, 0.016), Vector: |
-Components
#1: Protein | Mass: 33276.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.50 | ||||||||||||||||||||||||||||||||||||||||||
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: X11 / Wavelength: 0.8111 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8111 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→25 Å / Num. obs: 51154 / % possible obs: 99.1 % / Observed criterion σ(I): 13.53 / Redundancy: 5.24 % / Rmerge(I) obs: 0.0571 / Net I/σ(I): 4.34 |
Reflection shell | Resolution: 2.06→2.15 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.3209 / Mean I/σ(I) obs: 4.34 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 25 Å / Num. measured all: 270566 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OIH Resolution: 2.06→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.97 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 49.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→25 Å
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Refine LS restraints |
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