+Open data
-Basic information
Entry | Database: PDB / ID: 4p4t | ||||||
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Title | GDP-bound stalkless-MxA | ||||||
Components | Interferon-induced GTP-binding protein Mx1 | ||||||
Keywords | ANTIVIRAL PROTEIN/HYDROLASE / GTPase / dynamin-related protein / antiviral / mechano-enzyme / HYDROLASE / GTP-BINDING PROTEIN / ANTIVIRAL PROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / response to virus / defense response / ISG15 antiviral mechanism / Interferon alpha/beta signaling / microtubule binding / defense response to virus ...interleukin-27-mediated signaling pathway / response to type I interferon / negative regulation of viral genome replication / antiviral innate immune response / response to virus / defense response / ISG15 antiviral mechanism / Interferon alpha/beta signaling / microtubule binding / defense response to virus / nuclear membrane / microtubule / innate immune response / GTPase activity / apoptotic process / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rennie, M.L. / McKelvie, S.A. / Bulloch, E.M. / Kingston, R.L. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Structure / Year: 2014 Title: Transient Dimerization of Human MxA Promotes GTP Hydrolysis, Resulting in a Mechanical Power Stroke. Authors: Rennie, M.L. / McKelvie, S.A. / Bulloch, E.M. / Kingston, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p4t.cif.gz | 153.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p4t.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 4p4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/4p4t ftp://data.pdbj.org/pub/pdb/validation_reports/p4/4p4t | HTTPS FTP |
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-Related structure data
Related structure data | 4p4sC 4p4uSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40028.719 Da / Num. of mol.: 1 / Fragment: UNP residues 37-366 and 637-662 via LINKER GSGS / Mutation: C42S, C322S, C336S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P20591 | ||||
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#2: Chemical | ChemComp-GDP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | Chimera protein is stalkless-MxA made of UNP residues 37-366 and 637-662 via LINKER GSGS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 2.0-2.5M Ammonium sulfate, 0.2M AMPSO/KOH pH 9.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.05 Å / Num. obs: 17794 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P4U Resolution: 2.3→32.05 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.641 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.592 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→32.05 Å
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Refine LS restraints |
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