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Yorodumi- PDB-4lxw: L72V Epi-isozizaene synthase: Complex with Mg, inorganic pyrophos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lxw | ||||||
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Title | L72V Epi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate and benzyl triethyl ammonium cation | ||||||
Components | Epi-isozizaene synthase | ||||||
Keywords | LYASE / Class I terpene cyclase | ||||||
Function / homology | Function and homology information epi-isozizaene synthase / epi-isozizaene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å | ||||||
Authors | Li, R. / Chou, W. / Himmelberger, J.A. / Litwin, K. / Harris, G. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase. Authors: Li, R. / Chou, W.K. / Himmelberger, J.A. / Litwin, K.M. / Harris, G.G. / Cane, D.E. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lxw.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lxw.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lxw_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 4lxw_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 4lxw_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4lxw_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/4lxw ftp://data.pdbj.org/pub/pdb/validation_reports/lx/4lxw | HTTPS FTP |
-Related structure data
Related structure data | 4ltvC 4ltzC 4luuC 4lz0C 4lz3C 4lzcC 3kb9S 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, 1 molecules A
#1: Protein | Mass: 43701.984 Da / Num. of mol.: 1 / Mutation: L72V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: cyc1, SCO5222, SC7E4.19 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K499, epi-isozizaene synthase |
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-Non-polymers , 6 types, 249 molecules
#2: Chemical | #3: Chemical | ChemComp-POP / | #4: Chemical | ChemComp-BTM / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: A 4 uL drop of protein solution [8 mg/mL L72V EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 1 mM TCEP, 2 mM sodium pyrophosphate, 2 mM benzyltriethylammonium ...Details: A 4 uL drop of protein solution [8 mg/mL L72V EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 1 mM TCEP, 2 mM sodium pyrophosphate, 2 mM benzyltriethylammonium chloride (BTAC)] was added to a 4 uL drop of precipitant solution [100 mM Bis-Tris (pH 5.5), 25-28% polyethylene glycol 3350, 0.2 M (NH4)2SO4] and equilibrated against a 1 mL reservoir of precipitant solution at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.008 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2010 Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at3.3:1 demagnification. Mirror: ...Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification. |
Radiation | Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.092→50 Å / Num. obs: 22011 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12.204 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.479 / Rsym value: 0.301 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID: 3KB9 Resolution: 2.092→41.203 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.36 / 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 |
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Refinement step | Cycle: LAST / Resolution: 2.092→41.203 Å
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Refine LS restraints |
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LS refinement shell |
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