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Yorodumi- PDB-6k6a: Application of anti-helix antibodies in protein structure determi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k6a | |||||||||
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Title | Application of anti-helix antibodies in protein structure determination (8188cys-3LRHcys) | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / antibody / protein design | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Lee, J.O. / Jin, M.S. / Kim, J.W. / Kim, S. / Lee, H. / Cho, G.Y. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Application of antihelix antibodies in protein structure determination. Authors: Kim, J.W. / Kim, S. / Lee, H. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k6a.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k6a.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k6a_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 6k6a_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 6k6a_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 6k6a_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k6a ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k6a | HTTPS FTP |
-Related structure data
Related structure data | 6k3mC 6k64SC 6k65C 6k67C 6k68C 6k69C 6k6bC 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: 14143.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 8887.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P02976*PLUS #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: 1.78 Å3/Da / Density % sol: 30.79 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 45% PEG 4000, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 103 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21978 / % possible obs: 94.8 % / Redundancy: 2.8 % / Rpim(I) all: 0.035 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 1985 / Rpim(I) all: 0.091 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6K64 Resolution: 1.94→25.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.271 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.649 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→25.99 Å
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Refine LS restraints |
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