+Open data
-Basic information
Entry | Database: PDB / ID: 4ywo | ||||||
---|---|---|---|---|---|---|---|
Title | Mercuric reductase from Metallosphaera sedula | ||||||
Components | Mercuric reductase | ||||||
Keywords | OXIDOREDUCTASE / mercuric reductase / FAD | ||||||
Function / homology | Function and homology information mercury(II) reductase / mercury (II) reductase (NADP+) activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / detoxification of mercury ion / mercury ion binding / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Metallosphaera sedula (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Artz, J.H. / Zadvornyy, O.A. / White, S. / Peters, J.W. | ||||||
Citation | Journal: Front Bioeng Biotechnol / Year: 2015 Title: Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula. Authors: Artz, J.H. / White, S.N. / Zadvornyy, O.A. / Fugate, C.J. / Hicks, D. / Gauss, G.H. / Posewitz, M.C. / Boyd, E.S. / Peters, J.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ywo.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ywo.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ywo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ywo_validation.pdf.gz | 778.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ywo_full_validation.pdf.gz | 784.3 KB | Display | |
Data in XML | 4ywo_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 4ywo_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywo ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywo | HTTPS FTP |
-Related structure data
Related structure data | 1zk7S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50060.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Metallosphaera sedula (strain ATCC 51363 / DSM 5348) (archaea) Strain: ATCC 51363 / DSM 5348 / Gene: Msed_1241 / Production host: Escherichia coli (E. coli) / References: UniProt: A4YG49 | ||
---|---|---|---|
#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 55.85 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.085 M TRIS, 15% v/v glycerol, 14% w/v PEG400, 0.19 M LiSO4, and 20 mg/mL protein |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→70.65 Å / Num. obs: 71541 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.1687 / Rsym value: 0.1957 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.62→1.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / % possible all: 85.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZK7 Resolution: 1.62→70.65 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.522 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 24.543 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→70.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|