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Yorodumi- PDB-4l9y: Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l9y | ||||||
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Title | Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and propionyl-CoA | ||||||
Components | Malyl-CoA lyase | ||||||
Keywords | LYASE / TIM barrel | ||||||
Function / homology | Function and homology information malyl-CoA lyase / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å | ||||||
Authors | Zarzycki, J. / Kerfeld, C.A. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2013 Title: The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases. Authors: Zarzycki, J. / Kerfeld, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l9y.cif.gz | 374 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l9y.ent.gz | 299.9 KB | Display | PDB format |
PDBx/mmJSON format | 4l9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l9y ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l9y | HTTPS FTP |
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-Related structure data
Related structure data | 4l7zC 4l80C 4l9zC 1u5hS 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 36859.684 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: mcl1, RHOS4_03500, RSP_1771 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J5L6, malyl-CoA lyase |
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-Non-polymers , 5 types, 1582 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-1VU / | #5: Chemical | #6: 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: 2.43 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2 parts protein solution (3.0 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 3 parts buffer (0.1 M Tris-HCl, pH 8.5, 20% w/v PEG3350, 20 mM magnesium ...Details: 2 parts protein solution (3.0 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 3 parts buffer (0.1 M Tris-HCl, pH 8.5, 20% w/v PEG3350, 20 mM magnesium chloride), crystals soaked in crystallization mixture + 8 mM propionyl-CoA + 25% v/v glycerol for 3 minutes before plunging into liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.102→38.791 Å / Num. all: 113853 / Num. obs: 113853 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 15.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 Starting model: PDB ENTRY 1U5H Resolution: 2.102→38.791 Å / Occupancy max: 1 / Occupancy min: 0.76 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 22.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.67 Å2 / Biso mean: 23.5469 Å2 / Biso min: 5.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→38.791 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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