[English] 日本語
Yorodumi- PDB-3v7p: Crystal structure of amidohydrolase nis_0429 (target efi-500396) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v7p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of amidohydrolase nis_0429 (target efi-500396) from Nitratiruptor sp. sb155-2 | ||||||
Components | Amidohydrolase family protein | ||||||
Keywords | HYDROLASE / AMIDOHYDROLASE / IRON BINDING SITE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information aminodeoxyfutalosine deaminase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / menaquinone biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Nitratiruptor sp. SB155-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Amidohydrolase Nis_0429 (Target Efi-500319) from Nitratiruptor Sp. Sb155-2 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3v7p.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3v7p.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 3v7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v7p_validation.pdf.gz | 480 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3v7p_full_validation.pdf.gz | 483.6 KB | Display | |
Data in XML | 3v7p_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3v7p_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7p ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7p | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48413.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratiruptor sp. SB155-2 (bacteria) / Strain: SB155-2 / Gene: NIS_0429 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6Q234 |
---|
-Non-polymers , 8 types, 236 molecules
#2: Chemical | ChemComp-GOL / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-FE / | ||||||
#4: Chemical | ChemComp-BEZ / | ||||||
#5: Chemical | ChemComp-K / | ||||||
#6: Chemical | #7: Chemical | #8: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.01 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M MES, PH 6.0, 1M POTASSIUM SODIUM TARTRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→70 Å / Num. obs: 96466 / % possible obs: 99.6 % / Observed criterion σ(I): -5 / Redundancy: 4 % / Biso Wilson estimate: 16.967 Å2 / Rsym value: 0.051 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.3 / % possible all: 94.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.637 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.772 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
|