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Open data
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Basic information
Entry | Database: PDB / ID: 1zpv | ||||||
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Title | ACT domain protein from Streptococcus pneumoniae | ||||||
![]() | ACT domain protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ACT domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Uncharacterised protein family UPF0237, ACT-type / ACT domain / ACT domain profile. / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / : / UPF0237 protein SP_0238![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Hatzos, C. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: X-ray crystal structure of ACT domain protein from Streptococcus pneumoniae Authors: Osipiuk, J. / Hatzos, C. / Abdullah, J. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 51.2 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | the biological assembly is unknown |
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Components
#1: Protein | Mass: 10137.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-K / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M lithium sulfate, 0.1 M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 9, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 19284 / Num. obs: 19284 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.21 / Num. unique all: 1020 / % possible all: 73.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.997 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 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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