+Open data
-Basic information
Entry | Database: PDB / ID: 2xer | ||||||
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Title | Human PatL1 C-terminal domain (loop variant with sulfates) | ||||||
Components | PAT1 HOMOLOG 1 | ||||||
Keywords | RNA BINDING PROTEIN / MRNA DECAPPING / P-BODIES | ||||||
Function / homology | Function and homology information poly(G) binding / mRNA decay by 5' to 3' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / poly(U) RNA binding / P-body / cytoplasmic ribonucleoprotein granule / PML body / nuclear speck / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Tritschler, F. / Weichenrieder, O. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: The C-Terminal Alpha-Alpha Superhelix of Pat is Required for Mrna Decapping in Metazoa. Authors: Braun, J.E. / Tritschler, F. / Haas, G. / Igreja, C. / Truffault, V. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xer.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xer.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/2xer ftp://data.pdbj.org/pub/pdb/validation_reports/xe/2xer | HTTPS FTP |
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-Related structure data
Related structure data | 2xeqC 2xesSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28432.215 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 517-767 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA / Plasmid: MODIFIED PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q86TB9 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 664 TO GLY ...ENGINEERED | Sequence details | THE FIRST 5 AMINO ACIDS GPQDP RESULT FROM THE 5' CLONING SITE. RESIDUES 664-673 (QSAATPALSN) HAVE ...THE FIRST 5 AMINO ACIDS GPQDP RESULT FROM THE 5' CLONING SITE. RESIDUES 664-673 (QSAATPALSN | |
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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M TRIS, PH 8.5, 1.15 M AMMONIUM SULFATE, 0.15 M LITHIUM SULFATE, 8% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→47.2 Å / Num. obs: 18701 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 42.86 Å2 / Rsym value: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XES Resolution: 2.95→47.189 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 28.8 / Stereochemistry target values: ML Details: RESIDUES 512-516 AND 573-577 AND 704-708 AND 767 OF CHAIN A ARE DISORDERED. RESIDUES 512- -516 AND 573-577 AND 701-710 AND 767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 AND 701- ...Details: RESIDUES 512-516 AND 573-577 AND 704-708 AND 767 OF CHAIN A ARE DISORDERED. RESIDUES 512- -516 AND 573-577 AND 701-710 AND 767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 AND 701-709 AND 765-767 OF CHAIN C ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.225 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→47.189 Å
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Refine LS restraints |
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LS refinement shell |
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