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Open data
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Basic information
Entry | Database: PDB / ID: 1jm0 | |||||||||
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Title | CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL | |||||||||
![]() | PROTEIN (FOUR-HELIX BUNDLE MODEL) | |||||||||
![]() | DE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN | |||||||||
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: 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. #1: ![]() Title: 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. #2: ![]() Title: Tertiary Templates for the Design of Diiron Proteins Authors: Summa, C.M. / Lombardi, A. / Lewis, M. / DeGrado, W.F. #3: ![]() Title: De Novo Design and Structural Characterization of Proteins and Metalloproteins Authors: DeGrado, W.F. / Summa, C.M. / Pavone, V. / Nastri, F. / Lombardi, 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 | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.5 KB | Display | ![]() |
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Full document | ![]() | 416 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 5828.813 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: PEG 400 , Mn(CH3COO)2 , DMSO, Tris-HCl, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||
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 / Date: May 1, 2000 / 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: 1.7→20.1 Å / Num. all: 177455 / Num. obs: 33538 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.409 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 177455 |
Reflection shell | *PLUS % possible obs: 96.6 % / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: THEORETICAL MODEL Resolution: 1.7→20.1 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20.1 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 193.8 Å / Num. reflection obs: 31811 / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |