+Open data
-Basic information
Entry | Database: PDB / ID: 4mc3 | ||||||
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Title | Hedycaryol synthase in complex with Nerolidol | ||||||
Components | Putative sesquiterpene cyclase | ||||||
Keywords | LYASE / cyclase / terpenoid / Terpene alpha domain class I / helix break / helix dipol / surrogate | ||||||
Function / homology | Function and homology information (2Z,6E)-hedycaryol synthase / terpene synthase activity / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Kitasatospora setae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Baer, P. / Rabe, P. / Cirton, C. / Oliveira Mann, C. / Kaufmann, N. / Groll, M. / Dickschat, J. | ||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism. Authors: Baer, P. / Rabe, P. / Citron, C.A. / de Oliveira Mann, C.C. / Kaufmann, N. / Groll, M. / Dickschat, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mc3.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mc3.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 4mc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mc3_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 4mc3_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 4mc3_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4mc3_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/4mc3 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/4mc3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38701.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kitasatospora setae (bacteria) Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054 Gene: KSE_00200t, KSE_76540t / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: E4MYY0, Lyases; Carbon-oxygen lyases; Acting on phosphates |
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#2: Chemical | ChemComp-28U / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4M Sodium formiate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.855 Å / Num. all: 62111 / Num. obs: 61118 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.5→1.6 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.6 / % possible all: 96.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Hedycaryol Synthase experimentally phased with HgCl2 Resolution: 1.5→44.855 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.456 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 33.987 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44.855 Å
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Refine LS restraints |
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