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- PDB-6y3p: Crystal structure of the C-terminal domain from K. lactis Pby1, a... -

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Basic information

Entry
Database: PDB / ID: 6y3p
TitleCrystal structure of the C-terminal domain from K. lactis Pby1, an ATP-grasp enzyme interacting with the mRNA decapping enzyme Dcp2
ComponentsKLLA0B12012p
KeywordsLIGASE / ATP-grasp
Function / homology
Function and homology information


protein modification process => GO:0036211 / P-body / hydrolase activity
Similarity search - Function
Probable tubulin-tyrosine ligase / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile.
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsGraille, M.
Funding support France, 2items
OrganizationGrant numberCountry
ATIP-Avenir France
French National Research AgencyANR-11-BSV800902 France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Pby1 is a direct partner of the Dcp2 decapping enzyme.
Authors: Charenton, C. / Gaudon-Plesse, C. / Back, R. / Ulryck, N. / Cosson, L. / Seraphin, B. / Graille, M.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0B12012p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3975
Polymers47,0131
Non-polymers3844
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-39 kcal/mol
Surface area18750 Å2
Unit cell
Length a, b, c (Å)95.640, 95.640, 75.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-802-

SO4

21A-929-

HOH

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Components

#1: Protein KLLA0B12012p


Mass: 47012.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Gene: KLLA0_B12012g
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6CVH5
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium citrate tribasic pH 5.6; 0.5 M ammonium sulfate; 0.9 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→47.8 Å / Num. obs: 17920 / % possible obs: 99.1 % / Redundancy: 11.1 % / CC1/2: 0.999 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1710 / CC1/2: 0.507

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→41.41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.309 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.24 949 5.3 %RANDOM
Rwork0.188 ---
obs0.191 17914 98.7 %-
Displacement parametersBiso max: 166.99 Å2 / Biso mean: 65.05 Å2 / Biso min: 36.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.1461 Å20 Å20 Å2
2---1.1461 Å20 Å2
3---2.2923 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.3→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 20 32 3051
Biso mean--94.15 51.9 -
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1082SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes436HARMONIC5
X-RAY DIFFRACTIONt_it3098HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion388SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3450SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3098HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4199HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion21.74
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.262 146 5.15 %
Rwork0.211 2690 -
all0.213 2836 -
obs--98.23 %
Refinement TLS params.Method: refined / Origin x: 5.0519 Å / Origin y: -41.6967 Å / Origin z: 6.4729 Å
111213212223313233
T-0.13 Å2-0.0545 Å20.0153 Å2--0.0145 Å20.0774 Å2---0.0827 Å2
L0.9969 °2-0.2803 °2-0.4526 °2-0.665 °2-0.0459 °2--1.2725 °2
S0.0253 Å °-0.1523 Å °-0.1144 Å °0.0979 Å °0.0409 Å °0.0749 Å °0.0074 Å °-0.018 Å °-0.0662 Å °
Refinement TLS groupSelection details: { A|* }

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