[English] 日本語
Yorodumi- PDB-6w54: Crystal Structure of Gallic Acid Decarboxylase from Arxula adenin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w54 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans | ||||||
Components | Gallate decarboxylase | ||||||
Keywords | LYASE / Decarboxylase | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / 4-NITROCATECHOL / : / : / ARAD1C45716p Function and homology information | ||||||
Biological species | Blastobotrys adeninivorans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Zeug, M. / Marckovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J. | ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists. Authors: Zeug, M. / Markovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6w54.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6w54.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/6w54 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w54 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27241.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastobotrys adeninivorans (fungus) / Gene: AGDC1, GNLVRS02_ARAD1C45716g / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060TAG5 |
---|---|
#2: Chemical | ChemComp-4NC / |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-CO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, Potassium Formate, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 36574 / % possible obs: 88.5 % / Redundancy: 4.1 % / CC1/2: 0.95 / Rpim(I) all: 0.044 / Rrim(I) all: 0.094 / Rsym value: 0.094 / Net I/σ(I): 43 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 689 / CC1/2: 0.819 / Rpim(I) all: 0.236 / Rrim(I) all: 0.357 / Rsym value: 0.308 / % possible all: 33.8 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Unpublished Resolution: 1.5→41.7 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.93 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.7 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|