+Open data
-Basic information
Entry | Database: PDB / ID: 6qkm | |||||||||
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Title | Diallyl trisulfide inhibited sulfur oxygenase reductase | |||||||||
Components | (Sulfur oxygenase/reductase) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / SULFUR OXYGENASE REDUCTASE / 2-HIS-1-CARBOXYLATE FACIAL TRIAD / CYSTEINE PERSULPHURATION / BIOGEOCHEMICAL SULFUR CYCLE | |||||||||
Function / homology | sulfur oxygenase/reductase / sulfur oxygenase/reductase activity / Sulphur oxygenase reductase / Sulphur oxygenase reductase / Dimeric alpha-beta barrel / metal ion binding / cytoplasm / : / Sulfur oxygenase/reductase Function and homology information | |||||||||
Biological species | Acidianus ambivalens (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.102 Å | |||||||||
Authors | Frazao, C. / Klezin, A. / Poell, U. | |||||||||
Funding support | Portugal, Germany, 2items
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Citation | Journal: To Be Published Title: Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels Authors: Frazao, C. / Klezin, A. #1: Journal: Science / Year: 2006 Title: X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme. Authors: Urich, T. / Gomes, C.M. / Kletzin, A. / Frazao, C. #2: Journal: Front Microbiol / Year: 2011 Title: Substrate pathways and mechanisms of inhibition in the sulfur oxygenase reductase of acidianus ambivalens. Authors: Veith, A. / Urich, T. / Seyfarth, K. / Protze, J. / Frazao, C. / Kletzin, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qkm.cif.gz | 390.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qkm.ent.gz | 320.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qkm_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6qkm_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6qkm_validation.xml.gz | 69 KB | Display | |
Data in CIF | 6qkm_validation.cif.gz | 98.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/6qkm ftp://data.pdbj.org/pub/pdb/validation_reports/qk/6qkm | HTTPS FTP |
-Related structure data
Related structure data | 6qjcC 6qkaC 6qmvC 6qneC 6qo0C 6qpaC 2cb2S 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: 36541.262 Da / Num. of mol.: 2 / Mutation: TSY, CSS Source method: isolated from a genetically manipulated source Details: In chains A and D residues CYS_31 appear derivatized into TSY_31, residues CYS_101 appear derivatized into TSY_101 and residues CYS_104 appear derivatized into CSS_104, by chemical modification. Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase #2: Protein | Mass: 36509.195 Da / Num. of mol.: 4 / Mutation: CSS Source method: isolated from a genetically manipulated source Details: In chains B, C, E and F residues CYS_31 appear derivatized into TSY_31, residues CYS_101 appear derivatized into CSS_101 and residues CYS_104 appear derivatized into CSS_104, by chemical modification. Source: (gene. exp.) Acidianus ambivalens (archaea) / Gene: sor / Production host: Escherichia coli (E. coli) / References: UniProt: P29082, sulfur oxygenase/reductase #3: Chemical | ChemComp-FE / #4: 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: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→76.9 Å / Num. obs: 226318 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.048 / Rrim(I) all: 0.134 / Rsym value: 0.122 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 3.83 % / CC1/2: 0.555 / Rpim(I) all: 0.247 / Rrim(I) all: 1.065 / Rsym value: 0.896 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2CB2 Resolution: 2.102→76.9 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→76.9 Å
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Refine LS restraints |
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LS refinement shell |
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