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- PDB-3pf0: Crystal structure of an Imelysin-like protein (Psyc_1802) from PS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pf0 | ||||||
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Title | Crystal structure of an Imelysin-like protein (Psyc_1802) from PSYCHROBACTER ARCTICUM 273-4 at 2.15 A resolution | ||||||
![]() | Imelysin-like protein | ||||||
![]() | UNKNOWN FUNCTION / PUTATIVE METALLOENDOPEPTIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / Peptidase_M75 domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of an Imelysin-like protein (Psyc_1802) from PSYCHROBACTER ARCTICUM 273-4 at 2.15 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.7 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 422 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.9 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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Unit cell |
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Components on special symmetry positions |
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Details | CRYSTAL PACKING SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
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Components
#1: Protein | Mass: 38904.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT (RESIDUES 27-389) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 27-389) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→45.602 Å / Num. obs: 19285 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.316 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.99 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. THE FOLLOWING REGION HAS POOR DENSITY: A319-327. REGION A28-65 IS DISORDERED.
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Displacement parameters | Biso max: 126.13 Å2 / Biso mean: 47.343 Å2 / Biso min: 14.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→45.602 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.27 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 11.3256 Å / Origin y: 18.0514 Å / Origin z: -28.1989 Å
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Refinement TLS group | Selection details: { A|* } |