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Yorodumi- PDB-6qjz: Identificationand Characterization of an Oxalylfrom Grass pea (La... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qjz | ||||||
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Title | Identificationand Characterization of an Oxalylfrom Grass pea (Lathyrus sativusCoA-Synthetase L.) | ||||||
Components | oxalyl CoA-synthetase | ||||||
Keywords | LIGASE / adenylating ANL superfamily | ||||||
Function / homology | ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / ADENOSINE MONOPHOSPHATE / Putative oxalyl-CoA synthetase Function and homology information | ||||||
Biological species | Lathyrus sativus (chickling vetch) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dym, O. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Rsc Chem Biol / Year: 2022 Title: The identification and characterization of an oxalyl-CoA synthetase from grass pea ( Lathyrus sativus L.). Authors: Goldsmith, M. / Barad, S. / Peleg, Y. / Albeck, S. / Dym, O. / Brandis, A. / Mehlman, T. / Reich, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qjz.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qjz.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/6qjz ftp://data.pdbj.org/pub/pdb/validation_reports/qj/6qjz | HTTPS FTP |
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-Related structure data
Related structure data | 5ie2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56161.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lathyrus sativus (chickling vetch) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A3G8GC37*PLUS |
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#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M NaCl 25% Polyethylene glycol (PEG) 3,350 100 mM Tris pH 8.5. T |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.64 Å / Num. obs: 13429 / % possible obs: 99.97 % / Redundancy: 19.7 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.851 / Rpim(I) all: 0.1858 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.7→2.797 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 6.76 / Num. unique obs: 1294 / Rpim(I) all: 0.2636 / Χ2: 0.782 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IE2 Resolution: 2.7→47.64 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.892 / SU B: 12.828 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / 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: 20.496 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→47.64 Å
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Refine LS restraints |
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