+Open data
-Basic information
Entry | Database: PDB / ID: 6lkl | ||||||
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Title | Two-component system protein mediate signal transduction | ||||||
Components | ABC transporter, solute-binding proteinATP-binding cassette transporter | ||||||
Keywords | SIGNALING PROTEIN / two-component system / G6P sensor / signal transduction | ||||||
Function / homology | thiamine binding / thiamine transport / Bacterial extracellular solute-binding protein / thiamine pyrophosphate binding / Prokaryotic membrane lipoprotein lipid attachment site profile. / outer membrane-bounded periplasmic space / MALONIC ACID / ABC transporter, solute-binding protein Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.213 Å | ||||||
Authors | Wang, M. / Tao, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Interface switch mediates signal transmission in a two-component system. Authors: Wang, M. / Guo, Q. / Zhu, K. / Fang, B. / Yang, Y. / Teng, M. / Li, X. / Tao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lkl.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lkl.ent.gz | 190 KB | Display | PDB format |
PDBx/mmJSON format | 6lkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lkl ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lkl | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 29 - 322 / Label seq-ID: 1 - 294
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-Components
#1: Protein | Mass: 33754.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: E4U00_07700, EP54_06205, EQ90_12025, HMPREF3211_02751, NCTC10654_00249, NCTC10702_00414, RK64_01575 Production host: Escherichia coli (E. coli) / References: UniProt: X5DVD1 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.23 Å3/Da / Density % sol: 61.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 60% Tascimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 41995 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.21→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.411 / Num. unique obs: 4135 / CC1/2: 0.85 / Rpim(I) all: 0.259 / Rrim(I) all: 0.488 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.213→45.358 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.65 / Stereochemistry target values: ML
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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: 155.04 Å2 / Biso mean: 35.9202 Å2 / Biso min: 12.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.213→45.358 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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