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- PDB-1lt1: SLIDING HELIX INDUCED CHANGE OF COORDINATION GEOMETRY IN A MODEL ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lt1 | ||||||
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Title | SLIDING HELIX INDUCED CHANGE OF COORDINATION GEOMETRY IN A MODEL DI-MN(II) PROTEIN | ||||||
![]() | L13G-DF1 | ||||||
![]() | DE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN / SLIDING HELIX | ||||||
Function / homology | Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / : ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Costanzo, L. / Geremia, S. | ||||||
![]() | ![]() Title: Sliding helix and change of coordination geometry in a model di-MnII protein Authors: Degrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L. #1: ![]() Title: Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate-accessible Carboxylate-Bridged Dinuclear Metal Center Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. / Lombardi, A. #2: ![]() Title: Inaugural article: Retrostructural Analysis of Metalloproteins: Application to the Design of a Minimal Model for Diiron Proteins Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.6 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.9 KB | Display | ![]() |
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Full document | ![]() | 413.9 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jm0S S: Starting model for refinement |
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Similar structure data |
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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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4 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 5814.788 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This peptide was chemically synthetized. #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, MANGANESE ACETATE, BUFFER TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→6.03 Å / Num. all: 38634 / Num. obs: 38634 / % possible obs: 96.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5184 / Rsym value: 0.463 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 94932 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AB DIMER FROM THE STRUCTURE 1JM0 Resolution: 1.91→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 21.179 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.201 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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