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Yorodumi- PDB-3hyw: 3-D X-Ray structure of the sulfide:quinone oxidoreductase of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hyw | |||||||||
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Title | 3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone | |||||||||
Components | Sulfide-quinone reductase | |||||||||
Keywords | OXIDOREDUCTASE / MONOTOPIC MEMBRANE PROTEIN / FLAVOPROTEIN / POLYSULFUR | |||||||||
Function / homology | Function and homology information bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / quinone binding / nucleotide binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Marcia, M. / Ermler, U. / Peng, G.H. / Michel, H. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration Authors: Marcia, M. / Ermler, U. / Peng, G.H. / Michel, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hyw.cif.gz | 538.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hyw.ent.gz | 440.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hyw_validation.pdf.gz | 6.4 MB | Display | wwPDB validaton report |
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Full document | 3hyw_full_validation.pdf.gz | 6.4 MB | Display | |
Data in XML | 3hyw_validation.xml.gz | 112.3 KB | Display | |
Data in CIF | 3hyw_validation.cif.gz | 146 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hyw ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hyw | HTTPS FTP |
-Related structure data
Related structure data | 3hyvC 3hyxC 3h27 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 12 molecules ABCDEF
#1: Protein | Mass: 47566.984 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) AQUIFEX AEOLICUS (bacteria) / Strain: VF5 References: UniProt: O67931, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor #4: Sugar | ChemComp-LMT / |
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-Non-polymers , 6 types, 1187 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-DCQ / #5: Chemical | ChemComp-H2S / #6: Chemical | ChemComp-PS9 / #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE SIDE CHAIN OF CYS156 AND CYS347 ARE EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ...THE SIDE CHAIN OF CYS156 AND CYS347 ARE EXTENDED TO FORM A PUTATIVE POLYSULFUR |
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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: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 4% PEG 400, 2M AMMONIUM SULFATE, 0.1M NA-ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0015 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2008 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0015 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 194489 / % possible obs: 96.2 % / Redundancy: 4.74 % / Net I/σ(I): 13.17 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.86 % / Mean I/σ(I) obs: 1.86 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H27 3h27 Resolution: 2→20.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.395 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.168 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.976 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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