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Yorodumi- PDB-7m1s: Crystal structure of human guanylate-binding protein 2 (hGBP2) K5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m1s | |||||||||
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Title | Crystal structure of human guanylate-binding protein 2 (hGBP2) K51A mutant | |||||||||
Components | Guanylate-binding protein 2 | |||||||||
Keywords | HYDROLASE / large GTPase / immune signaling / NTPase / guanylate binding | |||||||||
Function / homology | Function and homology information positive regulation of AIM2 inflammasome complex assembly / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / endopeptidase inhibitor activity / molecular function inhibitor activity / defense response to protozoan / protein localization to nucleus / cellular response to interleukin-1 / activation of innate immune response / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...positive regulation of AIM2 inflammasome complex assembly / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / endopeptidase inhibitor activity / molecular function inhibitor activity / defense response to protozoan / protein localization to nucleus / cellular response to interleukin-1 / activation of innate immune response / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / cellular response to type II interferon / Interferon gamma signaling / Interferon alpha/beta signaling / cellular response to tumor necrosis factor / cytoplasmic vesicle / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-positive bacterium / defense response to bacterium / immune response / Golgi membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | |||||||||
Authors | Roy, S. / Wang, B. / Tian, Y. / Yin, Q. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of human guanylate-binding protein 2 (hGBP2) K51A mutant Authors: Roy, S. / Wang, B. / Tian, Y. / Yin, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m1s.cif.gz | 250.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m1s.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 7m1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m1s_validation.pdf.gz | 708.9 KB | Display | wwPDB validaton report |
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Full document | 7m1s_full_validation.pdf.gz | 724.3 KB | Display | |
Data in XML | 7m1s_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7m1s_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/7m1s ftp://data.pdbj.org/pub/pdb/validation_reports/m1/7m1s | HTTPS FTP |
-Related structure data
Related structure data | 1dg3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 67264.820 Da / Num. of mol.: 1 / Mutation: K51A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GBP2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P32456, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.12 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.7M NaH2PO4, 1.05M K2HPO4, 0.1M sodium acetate pH 3.8 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920126 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.920126 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 22461 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.056 / Rrim(I) all: 0.182 / Χ2: 1.076 / Net I/σ(I): 4.5 / Num. measured all: 211551 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DG3 Resolution: 2.91→45.64 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.75 / 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: 248.2 Å2 / Biso mean: 100.5535 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.91→45.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 78.5498 Å / Origin y: -1.0308 Å / Origin z: 261.0101 Å
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Refinement TLS group |
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