+Open data
-Basic information
Entry | Database: PDB / ID: 4q4u | ||||||
---|---|---|---|---|---|---|---|
Title | TvNiR in complex with sulfite, low dose data set | ||||||
Components | Eight-heme nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / 8 hemes c | ||||||
Function / homology | Function and homology information ammonium ion metabolic process / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / heme binding Similarity search - Function | ||||||
Biological species | Thioalkalivibrio nitratireducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Lazarenko, V.A. / Polyakov, K.M. / Trofimov, A.A. / Popov, A.N. / Tikhonova, T.V. / Tikhonov, A.V. / Popov, V.O. | ||||||
Citation | Journal: to be published Title: X-ray-induced changes in the active site structure of octaheme cytochrome c nitrite reductase and its substrate complexes Authors: Lazarenko, V.A. / Polyakov, K.M. / Trofimov, A.A. / Popov, A.N. / Tikhonova, T.V. / Tikhonov, A.V. / Popov, V.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4q4u.cif.gz | 264.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4q4u.ent.gz | 223.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4u ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4u | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59078.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thioalkalivibrio nitratireducens (bacteria) References: UniProt: Q5F2I3, UniProt: L0DSL2*PLUS |
---|
-Non-polymers , 7 types, 1215 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-SO3 / #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic, pH 5.6, 30% v/v 2-methil-2,4-pentanediol, 0.05 M sodium sulfite, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→15.48 Å / Num. obs: 304733 / % possible obs: 98.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.42 |
Reflection shell | Resolution: 1.62→1.68 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.37 / Num. unique all: 28742 / % possible all: 90 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→47.33 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.982 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.19 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→47.33 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20
|