+Open data
-Basic information
Entry | Database: PDB / ID: 4p4s | ||||||
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Title | GMPPCP-bound stalkless-MxA | ||||||
Components | (Interferon-induced GTP-binding protein Mx1) x 2 | ||||||
Keywords | ANTIVIRAL PROTEIN/HYDROLASE / GTPase / dynamin-related protein / antiviral / SIGNALING 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: 3.3 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 | 4p4s.cif.gz | 268.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p4s.ent.gz | 214.8 KB | Display | PDB format |
PDBx/mmJSON format | 4p4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/4p4s ftp://data.pdbj.org/pub/pdb/validation_reports/p4/4p4s | HTTPS FTP |
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-Related structure data
Related structure data | 4p4tC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Refine code: 0
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-Components
#1: Protein | Mass: 32600.695 Da / Num. of mol.: 1 / Fragment: UNP residues 43-361, 636-662 / Mutation: C42S,C322S,C336S, T636G, S637D, D638P, R640A 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: Protein | Mass: 38539.195 Da / Num. of mol.: 1 / Fragment: UNP residues 43-361, 636-662 / Mutation: C42S,C322S,C336S, T636G, S637D, D638P, R640A 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 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | Author states that chain A and chain B are from the same protein construct. However, in chain A ...Author states that chain A and chain B are from the same protein construct. However, in chain A where they were unable to determine the sequence register for some N-terminal and C-terminal residues, these residues were modeled as UNKs. The C-terminal UNKs are likely represent UNP residues 343-360. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 23-27% PEG 4000, 0.2 M EPPS/KOH pH 7.9, 0.5M glycerol |
-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: Oct 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→49.26 Å / Num. obs: 10950 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 19 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.9 / % 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: 3.3→49.26 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.85 / SU B: 85.04 / SU ML: 0.686 / Cross valid method: THROUGHOUT / ESU R Free: 0.71 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 83.846 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→49.26 Å
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Refine LS restraints |
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