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- PDB-2xes: Human PatL1 C-terminal domain (loop variant) -

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Basic information

Entry
Database: PDB / ID: 2xes
TitleHuman PatL1 C-terminal domain (loop variant)
ComponentsPROTEIN PAT1 HOMOLOG 1
KeywordsRNA 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 / PML body / cytoplasmic ribonucleoprotein granule / nuclear speck / RNA binding / cytosol
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1
Similarity search - Domain/homology
: / THIOCYANATE ION / Protein PAT1 homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsTritschler, F. / Weichenrieder, O.
CitationJournal: 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
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN PAT1 HOMOLOG 1
B: PROTEIN PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9258
Polymers57,6152
Non-polymers3116
Water9,350519
1
A: PROTEIN PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0796
Polymers28,8071
Non-polymers2715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8462
Polymers28,8071
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.650, 70.760, 134.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN PAT1 HOMOLOG 1 / PAT1-LIKE PROTEIN 1 / PATL1


Mass: 28807.371 Da / Num. of mol.: 2 / 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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 664 TO GLY
Has protein modificationY
Sequence detailsTHE 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) HAVE BEEN REPLACED BY G664 AND S665

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7 / Details: 12% PEG3350, 0.2 M KSCN, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788, 0.9788, 0.97922
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.979221
ReflectionResolution: 2.1→67 Å / Num. obs: 32014 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 26.11 Å2 / Rsym value: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.66 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXC/Dphasing
autoSHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→67.02 Å / SU ML: 0.27 / σ(F): 2.01 / Phase error: 21.66 / Stereochemistry target values: ML
Details: RESIDUES 512-516 AND 703-710 AND 767 OF CHAIN A ARE DISORDERED. RESIDUES 512-516 AND 704- -708 OF CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2323 1600 5 %
Rwork0.1986 --
obs0.2003 32009 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.652 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.6423 Å20 Å2-0 Å2
2--7.2835 Å20 Å2
3----6.6413 Å2
Refinement stepCycle: LAST / Resolution: 2.1→67.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 14 519 4345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083917
X-RAY DIFFRACTIONf_angle_d0.935291
X-RAY DIFFRACTIONf_dihedral_angle_d16.4391538
X-RAY DIFFRACTIONf_chiral_restr0.061626
X-RAY DIFFRACTIONf_plane_restr0.005670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.26661550.24772982X-RAY DIFFRACTION100
2.1751-2.26220.2721380.22073050X-RAY DIFFRACTION100
2.2622-2.36520.24411890.21432973X-RAY DIFFRACTION100
2.3652-2.48990.26621780.21213002X-RAY DIFFRACTION100
2.4899-2.64590.29191260.21533051X-RAY DIFFRACTION100
2.6459-2.85020.25561760.20963034X-RAY DIFFRACTION100
2.8502-3.1370.20251450.19673045X-RAY DIFFRACTION100
3.137-3.59090.23351590.18793039X-RAY DIFFRACTION99
3.5909-4.5240.2271700.1693069X-RAY DIFFRACTION99
4.524-67.05410.18561640.19433164X-RAY DIFFRACTION97

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