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- PDB-1rki: Structure of pag5_736 from P. aerophilum with three disulphide bonds -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rki | ||||||
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Title | Structure of pag5_736 from P. aerophilum with three disulphide bonds | ||||||
![]() | hypothetical protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / (beta-alpha-beta)x2 / beta-loop-beta-beta / CxxC motif | ||||||
Function / homology | PDO, CxxC motif / Protein of unknown function DUF3195 / Protein of unknown function (DUF3195) N-terminal domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beeby, M. / Ryttersgaard, C. / Boutz, D.R. / Perry, L.J. / Yeates, T.O. | ||||||
![]() | ![]() Title: The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles. Authors: Beeby, M. / Ryttersgaard, C. / Boutz, D.R. / Perry, L.J. / Yeates, T.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.5 KB | Display | ![]() |
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PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.4 KB | Display | ![]() |
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Full document | ![]() | 758.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11896.090 Da / Num. of mol.: 2 / Fragment: pag5_736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 95 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-P6G / | #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 8000, lithium sulphate, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.6→90 Å / Num. all: 28068 / Num. obs: 28068 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.125 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.495 / Num. unique all: 2174 / % possible all: 75 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.642 Å / 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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