+Open data
-Basic information
Entry | Database: PDB / ID: 4mc0 | ||||||
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Title | Hedycaryol apo | ||||||
Components | Putative sesquiterpene cyclase | ||||||
Keywords | LYASE / cyclase / terpenoid / Terpene alpha domain class I / helix break / helix dipol | ||||||
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: 2.7 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 | 4mc0.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mc0.ent.gz | 199.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/4mc0 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/4mc0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38701.473 Da / Num. of mol.: 2 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 #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: 3 Å3/Da / Density % sol: 58.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS, 1.6 M (NH4)2SO4, pH 8.0, 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: May 5, 2013 |
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: 2.7→30 Å / Num. all: 25308 / Num. obs: 24119 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HcS Nerolidol complex Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 26.638 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 57.583 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.768 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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