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Yorodumi- PDB-5i6g: Crystal structure of C-terminal variant 2 of Chaetomium thermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i6g | ||||||||||||
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Title | Crystal structure of C-terminal variant 2 of Chaetomium thermophilum acetyl-CoA carboxylase | ||||||||||||
Components | Acetyl-CoA carboxylase-like protein,Acetyl-CoA carboxylase-like protein | ||||||||||||
Keywords | LIGASE / Carboxylase / Fatty acid metabolism / Multienzyme / Carrier protein-dependent enzyme | ||||||||||||
Function / homology | Function and homology information biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||||||||
Authors | Hunkeler, M. / Stuttfeld, E. / Hagmann, A. / Imseng, S. / Maier, T. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Nat Commun / Year: 2016 Title: The dynamic organization of fungal acetyl-CoA carboxylase. Authors: Hunkeler, M. / Stuttfeld, E. / Hagmann, A. / Imseng, S. / Maier, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i6g.cif.gz | 861.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i6g.ent.gz | 716.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i6g ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i6g | HTTPS FTP |
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-Related structure data
Related structure data | 5i6eC 5i6fSC 5i6hC 5i6iC 5i87C C: citing same article (ref.) 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: 131906.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The crystallized construct contains amino acids 1114-2297 (aligned to accession code: G0S3L5). Due to formatting restrictions the SEQRES card was truncated C-terminally to residue R2261. C- ...Details: The crystallized construct contains amino acids 1114-2297 (aligned to accession code: G0S3L5). Due to formatting restrictions the SEQRES card was truncated C-terminally to residue R2261. C-terminal stretches after L2259 in chain A and R2261 in chain B could not be modeled unambiguously and were interpreted as poly-Ala/UNK residues. Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: CTHT_0021690 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S3L5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.34 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Hepes, Tacsimate, PEGMME5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→130.67 Å / Num. obs: 23225 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 197.83 Å2 / Rmerge(I) obs: 0.274 / Net I/σ(I): 6.35 |
Reflection shell | Resolution: 4.5→4.82 Å / Redundancy: 6.5 % / Rmerge(I) obs: 2.26 / Mean I/σ(I) obs: 1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I6F Resolution: 4.5→49.1 Å / Cor.coef. Fo:Fc: 0.9228 / Cor.coef. Fo:Fc free: 0.9207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.885
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Displacement parameters | Biso mean: 275.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.976 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→49.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.7 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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