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Yorodumi- PDB-5nen: Crystal structure of the soluble domain of LipC, a membrane fusio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nen | ||||||
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Title | Crystal structure of the soluble domain of LipC, a membrane fusion protein of a type I secretion system | ||||||
Components | Lipase C | ||||||
Keywords | HYDROLASE / lipase | ||||||
Function / homology | Function and homology information protein secretion / transmembrane transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.901 Å | ||||||
Authors | Murata, D. / Akutsu, M. / Takano, K. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain. Authors: Murata, D. / Okano, H. / Angkawidjaja, C. / Akutsu, M. / Tanaka, S.I. / Kitahara, K. / Yoshizawa, T. / Matsumura, H. / Kado, Y. / Mizohata, E. / Inoue, T. / Sano, S. / Koga, Y. / Kanaya, S. / Takano, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nen.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nen.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5nen ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5nen | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 49925.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: lipC / Production host: Escherichia coli (E. coli) / References: UniProt: Q54457 |
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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: 5.55 Å3/Da / Density % sol: 77.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Nov 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 28216 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 82.48 Å2 / Net I/σ(I): 28.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.901→41.346 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.42 / Phase error: 33.9 / Stereochemistry target values: MLHL
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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 | Biso max: 214.49 Å2 / Biso mean: 89.4909 Å2 / Biso min: 36.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.901→41.346 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 33.4012 Å / Origin y: 41.8423 Å / Origin z: 50.7918 Å
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Refinement TLS group |
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