+Open data
-Basic information
Entry | Database: PDB / ID: 7mfr | ||||||
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Title | Crystal Structure of a Fab fragment bound to peptide GGM | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Deubiquitinase Ubiquitin N-terminal Ubiquitination antibody tools UBE2W anti-GGX | ||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 Å | ||||||
Authors | Sudhamsu, J. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W. Authors: Davies, C.W. / Vidal, S.E. / Phu, L. / Sudhamsu, J. / Hinkle, T.B. / Chan Rosenberg, S. / Schumacher, F.R. / Zeng, Y.J. / Schwerdtfeger, C. / Peterson, A.S. / Lill, J.R. / Rose, C.M. / Shaw, ...Authors: Davies, C.W. / Vidal, S.E. / Phu, L. / Sudhamsu, J. / Hinkle, T.B. / Chan Rosenberg, S. / Schumacher, F.R. / Zeng, Y.J. / Schwerdtfeger, C. / Peterson, A.S. / Lill, J.R. / Rose, C.M. / Shaw, A.S. / Wertz, I.E. / Kirkpatrick, D.S. / Koerber, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mfr.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mfr.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 7mfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mfr_validation.pdf.gz | 470.3 KB | Display | wwPDB validaton report |
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Full document | 7mfr_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 7mfr_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 7mfr_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/7mfr ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mfr | HTTPS FTP |
-Related structure data
Related structure data | 4ma3S S: Starting model for refinement |
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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: Antibody | Mass: 23540.092 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 22904.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein/peptide | Mass: 263.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.58 Å3/Da / Density % sol: 73.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M Ammonium Sulfate, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9876 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.848→50 Å / Num. obs: 40950 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 75.28 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.039 / Rrim(I) all: 0.133 / Χ2: 1.401 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MA3 Resolution: 2.848→48.083 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.03 / 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 max: 143.38 Å2 / Biso mean: 78.5581 Å2 / Biso min: 44.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.848→48.083 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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