+Open data
-Basic information
Entry | Database: PDB / ID: 7dc7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of D12 Fab-ATP complex | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / ANTIBODY / COMPLEX / FAB | ||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Kawauchi, H. / Fukami, T.A. / Tatsumi, K. / Torizawa, T. / Mimoto, F. | ||||||
Citation | Journal: Cell Rep / Year: 2020 Title: Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment. Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. ...Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. / Susumu, H. / Sakashita, T. / Muraoka, T. / Aso, K. / Katada, H. / Tanaka, E. / Nakagawa, K. / Hasegawa, M. / Ayabe, M. / Yamamoto, T. / Tanba, S. / Ishiguro, T. / Kamikawa, T. / Nambu, T. / Kibayashi, T. / Azuma, Y. / Tomii, Y. / Kato, A. / Ozeki, K. / Murao, N. / Endo, M. / Kikuta, J. / Kamata-Sakurai, M. / Ishii, M. / Hattori, K. / Igawa, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dc7.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dc7.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dc7_validation.pdf.gz | 792.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dc7_full_validation.pdf.gz | 792.9 KB | Display | |
Data in XML | 7dc7_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 7dc7_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/7dc7 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/7dc7 | HTTPS FTP |
-Related structure data
Related structure data | 7dc8C 4nkiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24406.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 22656.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % / Mosaicity: 0.07 ° |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M HEPES, 32.5 %(w/v) Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.77→56.8 Å / Num. obs: 40596 / % possible obs: 92 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 14.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NKI Resolution: 1.77→41.072 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.27 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.66 Å2 / Biso mean: 26.0773 Å2 / Biso min: 12.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.77→41.072 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|