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Yorodumi- PDB-1hz5: CRYSTAL STRUCTURES OF THE B1 DOMAIN OF PROTEIN L FROM PEPTOSTREPT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hz5 | ||||||
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Title | CRYSTAL STRUCTURES OF THE B1 DOMAIN OF PROTEIN L FROM PEPTOSTREPTOCOCCUS MAGNUS, WITH A TYROSINE TO TRYPTOPHAN SUBSTITUTION | ||||||
Components | PROTEIN L | ||||||
Keywords | PROTEIN BINDING / Four stranded beta-sheet with central alpha helix / binds kappa light chain of immunoglobulins / zinc coordinated Histag | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Finegoldia magna (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | O'Neill, J.W. / Kim, D.E. / Baker, D. / Zhang, K.Y.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Authors: O'Neill, J.W. / Kim, D.E. / 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 | 1hz5.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hz5.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/1hz5 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/1hz5 | HTTPS FTP |
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-Related structure data
Related structure data | 1hz6SC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8052.908 Da / Num. of mol.: 2 / Fragment: B1 DOMAIN / Mutation: 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: 4.31 Å3/Da / Density % sol: 71.24 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M Zinc Accetate and MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
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: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 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: 1.8→30 Å / Num. all: 116074 / Num. obs: 26449 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.065 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1696 / Rsym value: 0.263 / % possible all: 98 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRYSTAL STRUCTURE OF B1 DOMAIN (Y47W), NON -HIS-TAG COORDINATE STRUCTURE (SEE 1HZ6) Resolution: 1.8→24.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1095659.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.9574 Å2 / ksol: 0.366238 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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