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Yorodumi- PDB-6zaw: Damage-free NO-bound copper nitrite reductase from Bradyrhizobium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zaw | ||||||
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Title | Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / product-bound / NO-bound / damage-free XFEL | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Authors: Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zaw.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zaw.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zaw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6zaw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6zaw_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 6zaw_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/6zaw ftp://data.pdbj.org/pub/pdb/validation_reports/za/6zaw | HTTPS FTP |
-Related structure data
Related structure data | 6zarC 6zasC 6zatC 6zauC 6zavC 6zaxC 6thfS 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 38086.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. (strain ORS 375) (bacteria) Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7, nitrite reductase (NO-forming) |
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#2: Polysaccharide |
-Non-polymers , 6 types, 515 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-EPE / | #6: Chemical | #7: Chemical | ChemComp-NO / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.67 Å3/Da / Density % sol: 53.9 % / Description: blue cubes |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 1.6/1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5/ pH 5.5 PH range: 5.0/5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→31 Å / Num. obs: 106311 / % possible obs: 100 % / Redundancy: 138.8 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.967 / R split: 0.034 / Rmerge(I) obs: 0.055 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.25→1.3 Å / Redundancy: 64.1 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13886 / CC1/2: 0.491 / R split: 0.491 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6THF Resolution: 1.3→30.87 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.719 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 63.53 Å2 / Biso mean: 19.054 Å2 / Biso min: 7.14 Å2
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Refinement step | Cycle: final / Resolution: 1.3→30.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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