+Open data
-Basic information
Entry | Database: PDB / ID: 6tpo | ||||||
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Title | Conformation of cd1 nitrite reductase NirS without bound heme d1 | ||||||
Components | Nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / cd1 nitrite reductase / NirS | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 Å | ||||||
Authors | Kluenemann, T. / Blankenfeldt, W. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Structure of heme d 1 -free cd 1 nitrite reductase NirS. Authors: Klunemann, T. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tpo.cif.gz | 311.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tpo.ent.gz | 256 KB | Display | PDB format |
PDBx/mmJSON format | 6tpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tpo_validation.pdf.gz | 829.3 KB | Display | wwPDB validaton report |
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Full document | 6tpo_full_validation.pdf.gz | 832 KB | Display | |
Data in XML | 6tpo_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 6tpo_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/6tpo ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tpo | HTTPS FTP |
-Related structure data
Related structure data | 6tsiC 1hzuS 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
#1: Protein | Mass: 60259.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) References: UniProt: P24474, nitrite reductase (NO-forming), hydroxylamine reductase |
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#2: Chemical | ChemComp-1PE / |
#3: Chemical | ChemComp-BU3 / ( |
#4: Chemical | ChemComp-HEC / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1M Phosphate/citrate pH4.2 40% (v/v) PEG300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.033217 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033217 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.86→69.28 Å / Num. obs: 54867 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Rrim(I) all: 0.16 / Net I/σ(I): 18 / Num. measured all: 1316645 / Scaling rejects: 44 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hzu Resolution: 1.861→54.364 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.22 Å2 / Biso mean: 34.4895 Å2 / Biso min: 14.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.861→54.364 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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