+Open data
-Basic information
Entry | Database: PDB / ID: 6c3m | |||||||||
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Title | Wild type structure of SiRHP | |||||||||
Components | Sulfite reductase [NADPH] hemoprotein beta-component | |||||||||
Keywords | METAL BINDING PROTEIN / redox / iron-sulfur cluster / Fe4-S4 cluster / siroheme / iron | |||||||||
Function / homology | Function and homology information assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Stroupe, M.E. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: The role of extended Fe4S4cluster ligands in mediating sulfite reductase hemoprotein activity. Authors: Cepeda, M.R. / McGarry, L. / Pennington, J.M. / Krzystek, J. / Stroupe, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c3m.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3m.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 6c3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3m ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3m | HTTPS FTP |
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-Related structure data
Related structure data | 6c3xC 6c3yC 6c3zC 1aopS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64091.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: cysI, b2763, JW2733 / Production host: Escherichia coli (E. coli) References: UniProt: P17846, assimilatory sulfite reductase (NADPH) |
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-Non-polymers , 5 types, 481 molecules
#2: Chemical | ChemComp-PO4 / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-SF4 / |
#5: Chemical | ChemComp-SRM / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.55 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.8 / Details: 65 mM Potassium Phosphate 18% PEG 8000 1 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39 Å / Num. obs: 68383 / % possible obs: 99.4 % / Redundancy: 9.7 % / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 3.8 % / Num. unique obs: 6514 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AOP Resolution: 1.5→38.6 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→38.6 Å
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Refine LS restraints |
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LS refinement shell |
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