[English] 日本語
Yorodumi- PDB-6m9r: Crystal structure of SznF from Streptomyces achromogenes var. str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m9r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 with a bound N(delta)-hydroxy-N(omega)-methyl-L-arginine intermediate | ||||||
Components | SznF | ||||||
Keywords | OXIDOREDUCTASE / non-heme iron-dependent / cupin domain / helix bundle / monooxygenase / N-nitrosation / L-arginine derivative / metal-bound / ligand-bound / anaerobic | ||||||
Function / homology | : / Chem-J9Y Function and homology information | ||||||
Biological species | Streptomyces achromogenes subsp. streptozoticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Rohac, R. / Mitchell, A.J. / Boal, A.K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nature / Year: 2019 Title: An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. Authors: Ng, T.L. / Rohac, R. / Mitchell, A.J. / Boal, A.K. / Balskus, E.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m9r.cif.gz | 408.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m9r.ent.gz | 332.2 KB | Display | PDB format |
PDBx/mmJSON format | 6m9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m9r_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6m9r_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 6m9r_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 6m9r_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9r ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9r | HTTPS FTP |
-Related structure data
Related structure data | 6m9sSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 471 / Label seq-ID: 4 - 471
|
-Components
#1: Protein | Mass: 53871.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria) Strain: NRRL 2697 / Gene: sznf / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: Oxidoreductases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 14-20% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.685→54.09 Å / Num. obs: 107050 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.089 / Net I/σ(I): 14.01 |
Reflection shell | Resolution: 1.69→1.79 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.52 / CC1/2: 0.825 / Rrim(I) all: 0.935 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6M9S Resolution: 1.69→54.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.233 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.095 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 10 cycles of TLS refinement using isotropic temperature factors (11 groups for each molecule of a.u.) followed by 10 cycles of maximum ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 10 cycles of TLS refinement using isotropic temperature factors (11 groups for each molecule of a.u.) followed by 10 cycles of maximum likelihood restrained refinement with 0.07 weighting term, 0.035 jelly-body refinement and automatically generated local NCS restraints.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.041 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.69→54.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|