[English] 日本語
Yorodumi- PDB-5h6s: Crystal structure of Hydrazidase S179A mutant complexed with a su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h6s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Hydrazidase S179A mutant complexed with a substrate | ||||||
Components | Amidase | ||||||
Keywords | HYDROLASE / amidase | ||||||
Function / homology | Amidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / amidase activity / 4-oxidanylbenzohydrazide / Amidase Function and homology information | ||||||
Biological species | Microbacterium sp. HM58-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Akiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K. / Sasaki, Y. / Takaya, N. / Yajima, S. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural basis of the substrate recognition of hydrazidase isolated from Microbacterium sp. strain HM58-2, which catalyzes acylhydrazide compounds as its sole carbon source Authors: Akiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K.I. / Sasaki, Y. / Takaya, N. / Yajima, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h6s.cif.gz | 357.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h6s.ent.gz | 288.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h6s_validation.pdf.gz | 478.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5h6s_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 5h6s_validation.xml.gz | 66.8 KB | Display | |
Data in CIF | 5h6s_validation.cif.gz | 96.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h6s ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h6s | HTTPS FTP |
-Related structure data
Related structure data | 5h6tSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 51565.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium sp. HM58-2 (bacteria) / Strain: HM58-2 / Gene: MHM582_3487 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A170QJP8 #2: Chemical | ChemComp-HDH / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole, 0.17 M LiSO4, 2M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 196526 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 5.2 / % possible all: 96.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H6T Resolution: 1.8→40.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.058 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.098 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.018 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→40.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|