+Open data
-Basic information
Entry | Database: PDB / ID: 1ps1 | ||||||
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Title | PENTALENENE SYNTHASE | ||||||
Components | PENTALENENE SYNTHASE | ||||||
Keywords | ANTIBIOTIC BIOSYNTHESIS / SESQUITERPENE CYCLASE / LYASE | ||||||
Function / homology | Function and homology information pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å | ||||||
Authors | Lesburg, C.A. / Christianson, D.W. | ||||||
Citation | Journal: Science / Year: 1997 Title: Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology. Authors: Lesburg, C.A. / Zhai, G. / Cane, D.E. / Christianson, D.W. #1: Journal: Protein Sci. / Year: 1995 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Recombinant Pentalenene Synthase Authors: Lesburg, C.A. / Lloyd, M.D. / Cane, D.E. / Christianson, D.W. #2: Journal: Biochemistry / Year: 1994 Title: Pentalenene Synthase. Purification, Molecular Cloning, Sequencing, and High-Level Expression in Escherichia Coli of a Terpenoid Cyclase from Streptomyces Uc5319 Authors: Cane, D.E. / Sohng, J.K. / Lamberson, C.R. / Rudnicki, S.M. / Wu, Z. / Lloyd, M.D. / Oliver, J.S. / Hubbard, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ps1.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ps1.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ps1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1ps1 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1ps1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.298373, -0.228446, -0.926707), Vector: |
-Components
#1: Protein | Mass: 38050.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: UC5319 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55012, EC: 4.6.1.5 #2: Chemical | ChemComp-PBM / | #3: 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: 3.4 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALLIZED FROM 1.5M AMMONIUM SULFATE, 100 MM HEPES, PH 7.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Lesburg, C.A., (1995) Protein Sci., 4, 2436. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Sep 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35 Å / Num. obs: 28128 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.056 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rsym value: 0.158 / % possible all: 57.7 |
Reflection | *PLUS Num. measured all: 70683 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Rmerge(I) obs: 0.158 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 52.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 17.4 Å2 / Rms dev position: 0.43 Å / Weight Biso : 44.4 / Weight position: 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.66 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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