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- PDB-1ovv: CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ovv | ||||||
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Title | CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II) | ||||||
![]() | FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II) | ||||||
![]() | 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: Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography. Authors: Geremia, S. / Di Costanzo, L. / Randaccio, L. / Engel, D.E. / Lombardi, A. / Nastri, F. / DeGrado, W.F. #1: ![]() Title: Sliding Helix Induced Change of Coordination Geomet Model Di-Mn(II) Protein Authors: Degrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L. #2: ![]() Title: Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate Accessible Carboxylate-Br Dinuclear Metal Center Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. / Lombardi, A. #3: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 57.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.5 KB | Display | ![]() |
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Full document | ![]() | 499.8 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 21.8 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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4 |
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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-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Peg 400, TRIS-HCl, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2002 / Details: MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: 1.2 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→33.3 Å / Num. obs: 6492 / % possible obs: 96.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.2 | |||||||||
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.573 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: UNCONVENTIANAL METHOD USING THE GROUP-SUBGROUP RELATION Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.903 / SU B: 31.395 / SU ML: 0.588 / Cross valid method: THROUGHOUT / ESU R Free: 0.611
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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