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Yorodumi- PDB-6hdy: Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hdy | ||||||
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Title | Crystal structure of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in the postadenylation state in complex with S3-HB-AMP | ||||||
Components | 2-hydroxyisobutyryl-CoA synthetase | ||||||
Keywords | LIGASE / 2-hydroxyisobutyrate CoA | ||||||
Function / homology | Function and homology information Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ligase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Aquincola tertiaricarbonis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zahn, M. / Rohwerder, T. / Strater, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle. Authors: Zahn, M. / Kurteva-Yaneva, N. / Schuster, J. / Krug, U. / Georgi, T. / Muller, R.H. / Rohwerder, T. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hdy.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hdy.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 6hdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hdy_validation.pdf.gz | 837.1 KB | Display | wwPDB validaton report |
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Full document | 6hdy_full_validation.pdf.gz | 839.2 KB | Display | |
Data in XML | 6hdy_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6hdy_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hdy ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hdy | HTTPS FTP |
-Related structure data
Related structure data | 6hdwC 6hdxC 6he0C 6he2C 2y4nS S: Starting model for refinement C: citing same article (ref.) |
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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: 55943.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquincola tertiaricarbonis (bacteria) / Gene: hcl / Production host: Escherichia coli (E. coli) References: UniProt: I3VE75, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases | ||
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#2: Chemical | ChemComp-3HL / ( | ||
#3: Chemical | ChemComp-8LQ / [[( | ||
#4: Chemical | #5: 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: 3.48 Å3/Da / Density % sol: 64.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05 M MES PH 6.0, 2.1 M LITHIUM SULFATE, 0.01 M MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.65 Å / Num. obs: 41011 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2 / Num. unique obs: 5801 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y4N Resolution: 2.2→24.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.164
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Displacement parameters | Biso mean: 50.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | S12: -0.5442 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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