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- PDB-5h6s: Crystal structure of Hydrazidase S179A mutant complexed with a su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h6s | ||||||
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Title | Crystal structure of Hydrazidase S179A mutant complexed with a substrate | ||||||
![]() | Amidase | ||||||
![]() | HYDROLASE / amidase | ||||||
Function / homology | Amidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / amidase activity / 4-oxidanylbenzohydrazide / Amidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Akiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K. / Sasaki, Y. / Takaya, N. / Yajima, S. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.5 KB | Display | ![]() |
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PDB format | ![]() | 288.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.4 KB | Display | ![]() |
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Full document | ![]() | 484.1 KB | Display | |
Data in XML | ![]() | 66.8 KB | Display | |
Data in CIF | ![]() | 96.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h6tSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51565.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HDH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: 1 / Resolution: 1.8→40.6 Å
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Refine LS restraints |
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