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Yorodumi- PDB-4rrp: Crystal Structure of the Fab complexed with antigen Asf1p, Northe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rrp | ||||||
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Title | Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS | ||||||
Function / homology | Histone chaperone ASF1-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / : Function and homology information | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS) / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16 Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Oconnell, P.T. / Maglaqui, M. / Bailey, L. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rrp.cif.gz | 660.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rrp.ent.gz | 545.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/4rrp ftp://data.pdbj.org/pub/pdb/validation_reports/rr/4rrp | HTTPS FTP |
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-Related structure data
Related structure data | 1qgcS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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Details | monomer,71.45 kD,90.4% |
-Components
#1: Antibody | Mass: 23590.217 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 25410.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 18059.211 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: AWRI796 / Gene: AWRI796_2536 / Production host: Escherichia coli (E. coli) / References: UniProt: E7KE71 #4: Chemical | ChemComp-PEG / | #5: 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: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 291 K / pH: 5.5 Details: Protein solution 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution ammonium acetate 0.1M, BIS-TRIS 0.1M, PEG 10,000 17%(w/v), microbatch under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 38.72 Å2 / Rmerge(I) obs: 0.086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QGC Resolution: 2.79→49.69 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 1.44 / Phase error: 25.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→49.69 Å
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Refine LS restraints |
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LS refinement shell |
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