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- PDB-2xeq: Human PatL1 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2xeq
TitleHuman PatL1 C-terminal domain
ComponentsPAT1 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
Protein PAT1 homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: PAT1 HOMOLOG 1,
B: PAT1 HOMOLOG 1,
C: PAT1 HOMOLOG 1,
D: PAT1 HOMOLOG 1,


Theoretical massNumber of molelcules
Total (without water)118,4174
Polymers118,4174
Non-polymers00
Water1448
1
A: PAT1 HOMOLOG 1,


Theoretical massNumber of molelcules
Total (without water)29,6041
Polymers29,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PAT1 HOMOLOG 1,


Theoretical massNumber of molelcules
Total (without water)29,6041
Polymers29,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PAT1 HOMOLOG 1,


Theoretical massNumber of molelcules
Total (without water)29,6041
Polymers29,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PAT1 HOMOLOG 1,


Theoretical massNumber of molelcules
Total (without water)29,6041
Polymers29,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.160, 108.570, 108.820
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
PAT1 HOMOLOG 1, / PAT1-LIKE PROTEIN 1 / PATL1


Mass: 29604.238 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 517-767
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 5 AMINO ACIDS GPQDP RESULT FROM THE 5' CLONING SITE.

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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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal growpH: 7.8
Details: 0.1 M BIS-TRIS-PROPANE, PH 7.8, 10% PEG3350, 0.2 M NA3-CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→43.9 Å / Num. obs: 22432 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 70.18 Å2 / Rsym value: 0.13 / Net I/σ(I): 9.1
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.88 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XES

2xes


Resolution: 3.1→43.919 Å / SU ML: 0.47 / σ(F): 1.21 / Phase error: 28.04 / Stereochemistry target values: ML
Details: RESIDUES 512-514 AND 573-576 AND 704-711 AND 766-767 OF CHAIN A ARE DISORDERED. RESIDUES 512-514 AND 573-577 AND 703-710 AND 766-767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 ...Details: RESIDUES 512-514 AND 573-576 AND 704-711 AND 766-767 OF CHAIN A ARE DISORDERED. RESIDUES 512-514 AND 573-577 AND 703-710 AND 766-767 OF CHAIN B ARE DISORDERED. RESIDUES 512-514 AND 574-577 AND 704-711 AND 766-767 OF CHAIN C ARE DISORDERED. RESIDUES 512-515 AND 663-670 AND 704-710 AND 766-767 OF CHAIN D ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2816 2122 5.1 %
Rwork0.2475 --
obs0.2491 41653 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.788 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 78 Å2
Baniso -1Baniso -2Baniso -3
1--11.6349 Å20 Å20 Å2
2--21.1583 Å20 Å2
3----9.5234 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 0 8 7690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057802
X-RAY DIFFRACTIONf_angle_d0.6810538
X-RAY DIFFRACTIONf_dihedral_angle_d12.7043043
X-RAY DIFFRACTIONf_chiral_restr0.0421257
X-RAY DIFFRACTIONf_plane_restr0.0071327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.21090.36122450.35973962X-RAY DIFFRACTION99
3.2109-3.33940.36342330.34063953X-RAY DIFFRACTION99
3.3394-3.49130.32662290.31633938X-RAY DIFFRACTION98
3.4913-3.67530.28862210.28213935X-RAY DIFFRACTION98
3.6753-3.90550.34771940.25973978X-RAY DIFFRACTION98
3.9055-4.20680.26822230.23613947X-RAY DIFFRACTION98
4.2068-4.62970.24532280.2213946X-RAY DIFFRACTION98
4.6297-5.29870.22641930.20483958X-RAY DIFFRACTION98
5.2987-6.6720.26681730.23693975X-RAY DIFFRACTION98
6.672-43.92330.23041830.20023939X-RAY DIFFRACTION97

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