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Yorodumi- PDB-3u9r: Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u9r | ||||||
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Title | Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC), beta subunit | ||||||
Components | Methylcrotonyl-CoA carboxylase, beta-subunit | ||||||
Keywords | LIGASE / carboxyltransferase / beta-beta-alpha superhelix | ||||||
Function / homology | Function and homology information isoprenoid catabolic process / methylcrotonoyl-CoA carboxylase activity / methylcrotonoyl-CoA carboxylase complex / L-leucine catabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Huang, C.S. / Tong, L. | ||||||
Citation | Journal: Nature / Year: 2012 Title: An unanticipated architecture of the 750-kDa {alpha}6{beta}6 holoenzyme of 3-methylcrotonyl-CoA carboxylase Authors: Huang, C.S. / Ge, P. / Zhou, Z.H. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u9r.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u9r.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 3u9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u9r ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9r | HTTPS FTP |
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-Related 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: 59670.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: liuB, PA2014 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I297, methylcrotonoyl-CoA carboxylase | ||
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#2: Chemical | ChemComp-1PE / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.87 % |
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Crystal grow | Temperature: 293 K / Method: under oil / pH: 6.5 Details: 1.6 M magnesium sulfate, 0.1 M MES, pH 6.5, UNDER OIL, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2010 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 148709 / Num. obs: 141517 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.7762 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.32 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1063730.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.5641 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→29.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file |
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