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- PDB-2xer: Human PatL1 C-terminal domain (loop variant with sulfates) -

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Basic information

Entry
Database: PDB / ID: 2xer
TitleHuman PatL1 C-terminal domain (loop variant with sulfates)
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: 2.95 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_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 / _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: PAT1 HOMOLOG 1
B: PAT1 HOMOLOG 1
C: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6817
Polymers85,2973
Non-polymers3844
Water79344
1
A: PAT1 HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)28,4321
Polymers28,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,4321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PAT1 HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7204
Polymers28,4321
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 100.100, 141.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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 ...ENGINEERED RESIDUE IN CHAIN A, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 664 TO GLY ENGINEERED RESIDUE IN CHAIN C, GLN 664 TO GLY
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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS, PH 8.5, 1.15 M AMMONIUM SULFATE, 0.15 M LITHIUM SULFATE, 8% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.95→3.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 98.1

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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: 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.
RfactorNum. reflection% reflection
Rfree0.2888 950 5.1 %
Rwork0.2471 --
obs0.2492 18674 98.73 %
Solvent computationShrinkage 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 parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.0384 Å20 Å20 Å2
2--4.6914 Å20 Å2
3----3.6529 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 20 44 5587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075622
X-RAY DIFFRACTIONf_angle_d0.7677587
X-RAY DIFFRACTIONf_dihedral_angle_d14.7232184
X-RAY DIFFRACTIONf_chiral_restr0.052904
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.10560.34911440.31912448X-RAY DIFFRACTION99
3.1056-3.30010.39351230.29962507X-RAY DIFFRACTION99
3.3001-3.55480.32111440.2862520X-RAY DIFFRACTION99
3.5548-3.91240.28651440.24672506X-RAY DIFFRACTION99
3.9124-4.47820.25111230.21292532X-RAY DIFFRACTION99
4.4782-5.64050.26211280.21872578X-RAY DIFFRACTION99
5.6405-47.1950.23671440.21742633X-RAY DIFFRACTION97

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