+Open data
-Basic information
Entry | Database: PDB / ID: 4bwx | ||||||
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Title | Structure of Neurospora crassa PAN3 pseudokinase mutant | ||||||
Components | PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3 | ||||||
Keywords | GENE REGULATION / DEADENYLASE / PAN2 / MIRNA / MRNA DECAY | ||||||
Function / homology | Function and homology information PAN complex / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / P-body / mRNA processing / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | NEUROSPORA CRASSA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Structure of the Pan3 Pseudokinase Reveals the Basis for Interactions with the Pan2 Deadenylase and the Gw182 Proteins Authors: Christie, M. / Boland, A. / Huntzinger, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bwx.cif.gz | 336.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bwx.ent.gz | 276 KB | Display | PDB format |
PDBx/mmJSON format | 4bwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bwx_validation.pdf.gz | 1012.7 KB | Display | wwPDB validaton report |
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Full document | 4bwx_full_validation.pdf.gz | 1021 KB | Display | |
Data in XML | 4bwx_validation.xml.gz | 29 KB | Display | |
Data in CIF | 4bwx_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/4bwx ftp://data.pdbj.org/pub/pdb/validation_reports/bw/4bwx | HTTPS FTP |
-Related structure data
Related structure data | 4bwkSC 4bwpC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.993, 0.085, 0.081), Vector: |
-Components
#1: Protein | Mass: 49380.316 Da / Num. of mol.: 2 Fragment: PSEUDOKINASE DOMAIN, COILED COIL, CTERMINAL KNOB DOMAIN, RESIDUES 234-656 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PNEA-NPM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SDP4 #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.7 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M HEPES PH 7.0, 15% PEG MONOMETHYL ETHER 5000 MME, 0.1 M POTASSIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→46.41 Å / Num. obs: 24793 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 65.23 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BWK Resolution: 2.85→45.156 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 29.36 / 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 mean: 89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→45.156 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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