+Open data
-Basic information
Entry | Database: PDB / ID: 1c76 | ||||||
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Title | STAPHYLOKINASE (SAK) MONOMER | ||||||
Components | STAPHYLOKINASE | ||||||
Keywords | HYDROLASE / BETA-GRASP FAMILY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Rao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y. | ||||||
Citation | Journal: To be published Title: Crystal Structure of Staphylokinase Dimer Offers New Clue to Reduction of Immunogenicity Authors: Rao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c76.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c76.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c76_validation.pdf.gz | 365.8 KB | Display | wwPDB validaton report |
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Full document | 1c76_full_validation.pdf.gz | 368.2 KB | Display | |
Data in XML | 1c76_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1c76_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c76 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c76 | 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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Unit cell |
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Details | It is proposed in the primary citation that the biological unit is a "head-to-tail" dimer (pdb entry 1c77). Two other dimers have been considered, with alpha helices at the interface (1c78) and beta sheets at the interface (1c79) respectively. However, the "head-to-tail" dimer interface allows for the formation of strong hydrophobic interactions as well as hydrogen bonds and is more stable than the other two forms. The authors have experimental evidence from site direct mutagenesis which supports their proposition. |
-Components
#1: Protein | Mass: 15487.585 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P68802, aureolysin |
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#2: 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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, pH 8.0, vapor diffusion/hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 6589 / Num. obs: 6589 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.182 / Num. unique all: 803 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Resolution: 2.25→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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