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Open data
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Basic information
Entry | Database: PDB / ID: 2eey | ||||||
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Title | Structure of GK0241 protein from Geobacillus kaustophilus | ||||||
![]() | Molybdopterin biosynthesis | ||||||
![]() | BIOSYNTHETIC PROTEIN / Molybdenium precursor bosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of GK0241 protein from Geobacillus kaustophilus Authors: Lokanath, N.K. / Pampa, K.J. / Kamiya, N. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.8 KB | Display | ![]() |
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PDB format | ![]() | 31.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.8 KB | Display | ![]() |
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Full document | ![]() | 428.9 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ekrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17492.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.12M Citrate-HCl, 0.25M Na formate, 0.1M NH(2)SO(4) and 22% PEG 4K, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 4, 2006 / Details: GRAPHITE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 15364 / Num. obs: 15314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 39 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EKR Resolution: 1.94→37.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4192177.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.4936 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→37.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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