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Open data
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Basic information
Entry | Database: PDB / ID: 1ilv | ||||||
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Title | Crystal Structure Analysis of the TM107 | ||||||
![]() | STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / new fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Beasley, S. / Evdokimova, E. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. Authors: Zhang, R.G. / Skarina, T. / Katz, J.E. / Beasley, S. / Khachatryan, A. / Vyas, S. / Arrowsmith, C.H. / Clarke, S. / Edwards, A. / Joachimiak, A. / Savchenko, 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 | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28622.887 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: 2.65 Å3/Da / Density % sol: 53.53 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: SBC-1 / Detector: CCD / Date: Mar 23, 2001 / 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: 2→50 Å / Num. all: 41136 / Num. obs: 41136 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.3 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4052 / % possible all: 99.8 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 79278 / % possible obs: 100 % / Num. measured all: 328134 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: wARP autotraced model Resolution: 2→46.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 295098.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: used mlhl refinement target in CNS package
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.62 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→46.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.244 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.341 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.33 |