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- PDB-2p6h: Crystal structure of hypothetical protein APE1520 from Aeropyrum ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p6h | ||||||
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Title | Crystal structure of hypothetical protein APE1520 from Aeropyrum pernix K1 | ||||||
![]() | Hypothetical protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Uncharacterized protein family UPF0047 signature. / YjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of hypothetical protein APE1520 from Aeropyrum pernix K1 Authors: Yamamoto, H. / 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 | ![]() | 68.7 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vphS 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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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 a trimer. |
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Components
#1: Protein | Mass: 14815.967 Da / Num. of mol.: 2 / Fragment: UNP residues 4-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: 0.1M HEPES, 1.5M Lithium Sulfate, pH7.5, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. all: 21471 / Num. obs: 21386 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.036 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 15 / Num. unique all: 2099 / Rsym value: 0.186 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VPH Resolution: 1.95→29.37 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→29.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024
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