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Yorodumi- PDB-1jml: Conversion of Monomeric Protein L to an Obligate Dimer by Computa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jml | ||||||
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Title | Conversion of Monomeric Protein L to an Obligate Dimer by Computational Protein Design | ||||||
Components | Protein L | ||||||
Keywords | PROTEIN BINDING / Domain Swapped Dimer / Four Stranded Beta-sheet with Central Alpha Helix / Carboxy-terminal Beta-strand Swapped. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Finegoldia magna (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | O'Neill, J.W. / Kuhlman, B. / Kim, D.E. / Zhang, K.Y.J. / Baker, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Conversion of monomeric protein L to an obligate dimer by computational protein design. Authors: Kuhlman, B. / O'Neill, J.W. / Kim, D.E. / Zhang, K.Y. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jml.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jml.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jml_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 1jml_full_validation.pdf.gz | 423.8 KB | Display | |
Data in XML | 1jml_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1jml_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/1jml ftp://data.pdbj.org/pub/pdb/validation_reports/jm/1jml | HTTPS FTP |
-Related structure data
Related structure data | 1hz5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8062.987 Da / Num. of mol.: 1 / Fragment: B1 DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51912 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.02 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 175mM Zinc Acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2000 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 8795 / Num. obs: 8777 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.076 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.8 / Num. unique all: 589 / Rsym value: 0.172 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 39485 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hz5 Resolution: 1.9→23.59 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1501114.86 / Data cutoff high rms absF: 1501114.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum Likelyhood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.4941 Å2 / ksol: 0.360826 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→23.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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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: 9.9 % / Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.234 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.204 |