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Yorodumi- PDB-4l80: Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l80 | ||||||
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Title | Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in complex with magnesium, oxalate, and propionyl-CoA | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / TIM barrel | ||||||
Function / homology | Function and homology information malyl-CoA lyase / carbon fixation by 3-hydroxypropionate cycle / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / oxaloacetate metabolic process / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chloroflexus aurantiacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.008 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 | 4l80.cif.gz | 449.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l80.ent.gz | 367.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l80_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4l80_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4l80_validation.xml.gz | 92.9 KB | Display | |
Data in CIF | 4l80_validation.cif.gz | 132.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/4l80 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l80 | HTTPS FTP |
-Related structure data
Related structure data | 4l7zSC 4l9yC 4l9zC 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 38415.344 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: OK-70-fl / Gene: Caur_0174, mcl / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A9WC35, UniProt: S5N020*PLUS, malyl-CoA lyase |
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-Non-polymers , 5 types, 1709 molecules
#2: Chemical | ChemComp-1VU / #3: Chemical | ChemComp-OXL / #4: Chemical | ChemComp-MG / #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: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M sodium cacodylate, pH 5.5, 20% w/v PEG4000) + 1 part ...Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M sodium cacodylate, pH 5.5, 20% w/v PEG4000) + 1 part substrate solution (20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride, 20 mM propionyl-CoA, 25 mM sodium oxalate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.008→37.93 Å / Num. all: 138647 / Num. obs: 138647 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rsym value: 0.106 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 4L7Z Resolution: 2.008→37.93 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.2 / σ(F): 1.18 / Phase error: 19.96 / 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: 97.91 Å2 / Biso mean: 28.2585 Å2 / Biso min: 8.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.008→37.93 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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