+Open data
-Basic information
Entry | Database: PDB / ID: 1k53 | ||||||
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Title | Monomeric Protein L B1 Domain with a G15A Mutation | ||||||
Components | Protein L | ||||||
Keywords | PROTEIN BINDING / Protein L B1 domain / strained beta-hairpin turn / positive phi angles / domain swapping / amyloid formation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Finegoldia magna (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | O'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y.J. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Authors: O'Neill, J.W. / Kim, D.E. / Johnsen, K. / Baker, D. / Zhang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k53.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k53.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k53 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k53 | HTTPS FTP |
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-Related structure data
Related structure data | 1k50C 1k51C 1k52C 1hz5S S: Starting model for refinement C: citing same article (ref.) |
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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: 8066.934 Da / Num. of mol.: 2 / Fragment: B1 Domain (Residues 111-173) / Mutation: G15A, Y47W 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 #2: Chemical | ChemComp-ZN / #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: 4.32 Å3/Da / Density % sol: 71.54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 225mM ZnOAC, 50mM Cacadylate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||||||||||||||||||||||||||
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: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 21, 2000 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 16917 / Num. obs: 16901 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.079 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1118 / Rsym value: 0.386 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 109046 / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS Rmerge(I) obs: 0.428 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1HZ5 Resolution: 2.1→24.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1267659.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.9449 Å2 / ksol: 0.358714 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor all: 0.23 / Rfactor obs: 0.213 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2129 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.241 / Rfactor Rwork: 0.213 |