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Yorodumi- PDB-6r6n: Recombinantly produced Kusta0087/Kusta0088 Complex, C32M/C101M mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r6n | ||||||
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Title | Recombinantly produced Kusta0087/Kusta0088 Complex, C32M/C101M mutant | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Heme-c / cystein ligation | ||||||
Function / homology | Function and homology information electron transport chain / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Kuenenia stuttgartiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Akram, M. / Barends, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: A nitric oxide-binding heterodimeric cytochromeccomplex from the anammox bacteriumKuenenia stuttgartiensisbinds to hydrazine synthase. Authors: Akram, M. / Reimann, J. / Dietl, A. / Menzel, A. / Versantvoort, W. / Kartal, B. / Jetten, M.S.M. / Barends, T.R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r6n.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r6n.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 6r6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r6n ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r6n | HTTPS FTP |
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-Related structure data
Related structure data | 6r6mSC 6r6oC 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: 12431.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: KSMBR1_3082, kusta0087 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1Q7P4 | ||
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#2: Protein | Mass: 10889.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: KSMBR1_3083, kusta0088 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1Q7P3 | ||
#3: Chemical | #4: 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: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20-25% PEG3000, 0.1 M Na-citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→63 Å / Num. obs: 18722 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rrim(I) all: 0.123 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 6.4 % / Num. unique obs: 2465 / Rrim(I) all: 0.736 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6R6M Resolution: 2→45.66 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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