+Open data
-Basic information
Entry | Database: PDB / ID: 1nvo | ||||||
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Title | Solution structure of a four-helix bundle model, apo-DF1 | ||||||
Components | Homodimeric Alpha2 Four-Helix Bundle | ||||||
Keywords | UNKNOWN FUNCTION / De Novo Protein Design / Alpha-Helical Bundle / Diiron Protein Model | ||||||
Function / homology | Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Function and homology information | ||||||
Method | SOLUTION NMR / Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization | ||||||
Authors | Maglio, O. / Nastri, F. / Pavone, V. / Lombardi, A. / DeGrado, W.F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Preorganization of molecular binding sites in designed diiron proteins Authors: Maglio, O. / Nastri, F. / Pavone, V. / Lombardi, A. / DeGrado, W.F. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 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: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1999 Title: Tertiary Templates for the Design of Diiron Protein Authors: Summa, C.M. / Lombardi, A. / Lewis, M. / DeGrado, W.F. #3: Journal: J.Am.Chem.Soc. / Year: 2001 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. #4: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003 Title: Sliding Helix and Change of Coordination Geometry in a Model di-Mn(II) Protein Authors: DeGrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nvo.cif.gz | 464.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nvo.ent.gz | 404 KB | Display | PDB format |
PDBx/mmJSON format | 1nvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nvo_validation.pdf.gz | 370.8 KB | Display | wwPDB validaton report |
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Full document | 1nvo_full_validation.pdf.gz | 539.4 KB | Display | |
Data in XML | 1nvo_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1nvo_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nvo ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nvo | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5870.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques |
-Sample preparation
Details | Contents: 1.0 mM protein concentration; 90% H2O, 10% DMSO / Solvent system: 90% H2O, 10% DMSO |
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Sample conditions | pH: 4.0 / Pressure: Ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 14 |