[English] 日本語
Yorodumi- PDB-5uao: Crystal structure of MibH, a lathipeptide tryptophan 5-halogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uao | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MibH, a lathipeptide tryptophan 5-halogenase | ||||||
Components | Tryptophane-5-halogenase | ||||||
Keywords | OXIDOREDUCTASE / halogenase / lanthipeptide / tryptophan / NAI-107 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Microbispora sp. ATCC PTA-5024 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Cogan, D.P. / Nair, S.K. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis. Authors: Ortega, M.A. / Cogan, D.P. / Mukherjee, S. / Garg, N. / Li, B. / Thibodeaux, G.N. / Maffioli, S.I. / Donadio, S. / Sosio, M. / Escano, J. / Smith, L. / Nair, S.K. / van der Donk, W.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uao.cif.gz | 434.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uao.ent.gz | 349.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/5uao ftp://data.pdbj.org/pub/pdb/validation_reports/ua/5uao | HTTPS FTP |
---|
-Related structure data
Related structure data | 2wetS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59237.973 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbispora sp. ATCC PTA-5024 (bacteria) Gene: mlbH, MPTA5024_21495 / Production host: Escherichia coli (E. coli) / References: UniProt: W2EQU4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% MPD, 12.5% PEG 3.35K, 0.1 M MES/imidazole pH 6.5, and 0.09 M NPS (1:1:1 NaNO3, Na2HPO4, (NH4)2SO4) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→87.38 Å / Num. obs: 170761 / % possible obs: 97.8 % / Redundancy: 7.9 % / Net I/σ(I): 16.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WET Resolution: 1.88→87.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.767 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / 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: 36.207 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.88→87.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|