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Yorodumi- PDB-6lvu: Crystal structure of apo acyl carrier protein from Thermotoga maritima -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lvu | ||||||
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Title | Crystal structure of apo acyl carrier protein from Thermotoga maritima | ||||||
Components | Acyl carrier protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / acyl carrier protein | ||||||
Function / homology | Function and homology information lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.294 Å | ||||||
Authors | Lee, Y. / Lee, W.C. / Kim, Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Characterization of an ACP fromThermotoga maritima: Insights into Hyperthermal Adaptation. Authors: Lee, Y. / Jang, A. / Jeong, M.C. / Park, N. / Park, J. / Lee, W.C. / Cheong, C. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lvu.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lvu.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lvu_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 6lvu_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 6lvu_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6lvu_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/6lvu ftp://data.pdbj.org/pub/pdb/validation_reports/lv/6lvu | HTTPS FTP |
-Related structure data
Related structure data | 6lvtC 2ehsS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 80 / Label seq-ID: 3 - 80
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-Components
#1: Protein | Mass: 8905.988 Da / Num. of mol.: 2 / Fragment: ACP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: acpP / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZD0 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.4 / Details: 0.2M zinc acetate dihydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.294→50 Å / Num. obs: 6764 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.07 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Χ2: 3.869 / Net I/σ(I): 22.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EHS Resolution: 2.294→28.367 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.24 Å2 / Biso mean: 27.4444 Å2 / Biso min: 9.36 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.294→28.367 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
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