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Yorodumi- PDB-5h92: Crystal structure of the complex between maize Sulfite Reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h92 | |||||||||
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Title | Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-3 crystal | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / Ferredoxin / Sulfite reductase / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | |||||||||
Function / homology | Function and homology information plastid chromosome packaging / assimilatory sulfite reductase (ferredoxin) / sulfide oxidation / chloroplast nucleoid / stromule / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / chloroplast stroma ...plastid chromosome packaging / assimilatory sulfite reductase (ferredoxin) / sulfide oxidation / chloroplast nucleoid / stromule / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / chloroplast stroma / response to light stimulus / response to cold / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / electron transfer activity / negative regulation of DNA-templated transcription / heme binding / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||
Authors | Kurisu, G. / Nakayama, M. / Hase, T. | |||||||||
Citation | Journal: J.Biochem. / Year: 2016 Title: Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. Authors: Kim, J.Y. / Nakayama, M. / Toyota, H. / Kurisu, G. / Hase, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h92.cif.gz | 496 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h92.ent.gz | 405.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h92_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5h92_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5h92_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 5h92_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h92 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h92 | HTTPS FTP |
-Related structure data
Related structure data | 5h8vSC 5h8yC 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 65077.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: SIR / Production host: Escherichia coli (E. coli) References: UniProt: O23813, assimilatory sulfite reductase (ferredoxin) #2: Protein | | Mass: 10518.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: FDX1, pFD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27787 |
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-Non-polymers , 6 types, 390 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FES / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG4000, 0.05M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 20, 2007 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 579880 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 34.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H8V Resolution: 2.08→43.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.06 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.181 / 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: 38.295 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→43.27 Å
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Refine LS restraints |
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