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Yorodumi- PDB-1f4m: P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f4m | ||||||
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Title | P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD. | ||||||
Components | ROP ALA2ILE2-6 | ||||||
Keywords | TRANSCRIPTION / Rop / dimer / homodimer / helix-turn-helix / transcription regulation / hydrophobic core packing / thermodynamic stability | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Willis, M.A. / Bishop, B. / Regan, L. / Brunger, A.T. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core. Authors: Willis, M.A. / Bishop, B. / Regan, L. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f4m.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f4m.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f4m_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 1f4m_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 1f4m_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1f4m_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f4m ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f4m | HTTPS FTP |
-Related structure data
-Links
-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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Details | The biological assembly is a dimer of which there are three in the asymmetric unit |
-Components
#1: Protein | Mass: 7053.767 Da / Num. of mol.: 6 / Mutation: M1G,A8I,T19A,L22I,L26A,Q34I,C38A,L41I,L48I,C52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid details: PMR101 / Production host: Escherichia coli (E. coli) / References: UniProt: P03051 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, calcium chloride, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54128 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54128 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.66 Å / Num. all: 20062 / Num. obs: 20062 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.238 / Num. unique all: 909 / % possible all: 40 |
Reflection shell | *PLUS % possible obs: 63.5 % |
-Processing
Software |
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Refinement | Resolution: 2.25→45.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2893541.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.39 Å2 / ksol: 0.449 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→45.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor obs: 0.233 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.303 |