+Open data
-Basic information
Entry | Database: PDB / ID: 7eb6 | ||||||
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Title | Crystal structure of GTP-binding protein-like domain of AGAP1 | ||||||
Components | Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 | ||||||
Keywords | CELL ADHESION / AGAP1 / GTP-binding protein-like domain / leukemia | ||||||
Function / homology | Function and homology information GTPase activator activity / phospholipid binding / positive regulation of GTPase activity / protein transport / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.014 Å | ||||||
Authors | Cheng, N. / Zhang, H. / Zhang, S. / Ma, X. / Meng, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Crystal structure of the GTP-binding protein-like domain of AGAP1. Authors: Cheng, N. / Zhang, H. / Zhang, S. / Ma, X. / Meng, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eb6.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eb6.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 7eb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7eb6 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7eb6 | HTTPS FTP |
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-Related structure data
Related structure data | 2iwrS 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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Unit cell |
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-Components
#1: Protein | Mass: 19354.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGAP1, CENTG2, KIAA1099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPQ3 |
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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: 3.13 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 3.014→35.493 Å / Num. obs: 9136 / % possible obs: 99.57 % / Redundancy: 5.9 % / CC1/2: 0.949 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.014→3.122 Å / Num. unique obs: 458 / CC1/2: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IWR Resolution: 3.014→35.493 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.07 / 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: 138.27 Å2 / Biso mean: 43.3223 Å2 / Biso min: 10.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.014→35.493 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 14.2952 Å / Origin y: -18.0363 Å / Origin z: -19.1304 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 69 through 233) |