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- PDB-1ryl: The Crystal Structure of a Protein of Unknown Function YfbM from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ryl | ||||||
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Title | The Crystal Structure of a Protein of Unknown Function YfbM from Escherichia coli | ||||||
![]() | Hypothetical protein yfbM | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | YfbM-like super family / Protein of unknown function DUF1877 / YfbM-like super family / Domain of unknown function (DUF1877) / Hypothetical protein yfbM fold / 3-Layer(aba) Sandwich / Alpha Beta / Protein YfbM![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: 1.6A crystal structure of a hypothetical protein yfbM from E. coli Authors: Zhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 58.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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Details | The biological assembly is a monomer. MolA and MolB represent two molecules in asymmetric unit. |
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Components
#1: Protein | Mass: 19040.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M MgCl2, 0.1 M HEPES, 30%PEG3350, 8% Ethanol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 12, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. all: 84444 / Num. obs: 78702 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.37 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.85 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.223 / Num. unique all: 4690 / % possible all: 55.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.6538 Å2 / ksol: 0.410761 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→30.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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