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Yorodumi- PDB-5ikl: Crystal structure of P. aeruginosa geranyl-CoA carboxylase (GCC),... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ikl | ||||||||||||
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Title | Crystal structure of P. aeruginosa geranyl-CoA carboxylase (GCC), beta subunit | ||||||||||||
Components | Geranyl-CoA carboxylase, beta-subunit | ||||||||||||
Keywords | LIGASE / Carboxylase / organic acid metabolism | ||||||||||||
Function / homology | Function and homology information geranoyl-CoA carboxylase activity / terpene catabolic process / methylcrotonoyl-CoA carboxylase complex / L-leucine catabolic process / fatty acid biosynthetic process Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||||||||
Authors | Huang, C.S. / Jurado, A.R. / Tong, L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2015 Title: Structure and substrate selectivity of the 750-kDa alpha6beta6 holoenzyme of geranyl-CoA carboxylase Authors: Jurado, A.R. / Huang, C.S. / Zhang, X. / 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 | 5ikl.cif.gz | 281.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikl.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ikl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikl ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57263.141 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: atuC, PA2888 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZV9 #2: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl (pH 8.0), 60% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 71918 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Χ2: 1.035 / Net I/av σ(I): 15.707 / Net I/σ(I): 11.7 / Num. measured all: 322453 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.195 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.963 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.29 Å2 / Biso mean: 65.984 Å2 / Biso min: 30.88 Å2
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Refinement step | Cycle: final / Resolution: 2.4→47.195 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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