+Open data
-Basic information
Entry | Database: PDB / ID: 5o1m | |||||||||
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Title | Structure of Latex Clearing Protein LCP in the closed state | |||||||||
Components | Rubber oxygenase | |||||||||
Keywords | OXIDOREDUCTASE / heme / oxygenase / rubber / biopolymers | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases) / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / isoprenoid catabolic process / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Streptomyces sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Ilcu, L. / Roether, W. / Birke, J. / Brausemann, A. / Einsle, O. / Jendrossek, D. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structural and Functional Analysis of Latex Clearing Protein (Lcp) Provides Insight into the Enzymatic Cleavage of Rubber. Authors: Ilcu, L. / Rother, W. / Birke, J. / Brausemann, A. / Einsle, O. / Jendrossek, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o1m.cif.gz | 291.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o1m.ent.gz | 236.5 KB | Display | PDB format |
PDBx/mmJSON format | 5o1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o1m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5o1m_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5o1m_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 5o1m_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/5o1m ftp://data.pdbj.org/pub/pdb/validation_reports/o1/5o1m | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 35 - 401 / Label seq-ID: 4 - 370
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-Components
#1: Protein | Mass: 40377.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (strain K30) (bacteria) Gene: lcp / Plasmid: p4782.1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q3L8N0, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases) #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16 % (w/v) PEG 3350, 0.2 M L-proline, 0.1 M HEPES/NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.73672 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.73672 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→61.45 Å / Num. obs: 30914 / % possible obs: 87.2 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.039 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2566 / CC1/2: 0.932 / Rpim(I) all: 0.18 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→61.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.673 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.231 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.9 Å2 / Biso mean: 38.276 Å2 / Biso min: 19.24 Å2
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Refinement step | Cycle: final / Resolution: 2.2→61.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 23254 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / 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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