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- PDB-6k1w: Crystal structure of Rhodothermus marinus substrate-binding prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k1w | |||||||||
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Title | Crystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5 | |||||||||
![]() | ABC-type uncharacterized transport system periplasmic component-like protein | |||||||||
![]() | TRANSPORT PROTEIN / substrate binding protein / SBP / substrate binding domain | |||||||||
Function / homology | ABC transporter, substrate-binding protein / ABC transporter substrate binding protein / ABC-type uncharacterized transport system periplasmic component-like protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nam, K.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5 Authors: Nam, K.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 30.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5z6vS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18394.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43812 / DSM 4252 / R-10 / Gene: Rmar_2176 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Magnesium chloride, BIS-Tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.29 Å / Num. obs: 21337 / % possible obs: 97.7 % / Redundancy: 5.4 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 40.125 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 5.57 / Num. unique obs: 1064 / CC1/2: 0.888 / Rpim(I) all: 0.17 / Rrim(I) all: 0.39 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z6V Resolution: 1.5→37.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.403 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 128.55 Å2 / Biso mean: 22.614 Å2 / Biso min: 9.05 Å2
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Refinement step | Cycle: final / Resolution: 1.5→37.29 Å
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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