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- PDB-4pqz: Crystal structure of swt1 C-terminal domain from yeast -

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Basic information

Entry
Database: PDB / ID: 4pqz
TitleCrystal structure of swt1 C-terminal domain from yeast
ComponentsTranscriptional protein SWT1
KeywordsTRANSCRIPTION / HEPN like fold
Function / homology
Function and homology information


nuclear mRNA surveillance of mRNP export / RNA endonuclease activity / nucleus / cytoplasm
Similarity search - Function
: / : / Transcriptional protein SWT1, C-terminal domain / PIN domain / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
Transcriptional protein SWT1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPeng, S.X. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1.
Authors: Peng, S. / Zhou, K. / Wang, W. / Gao, Z. / Dong, Y. / Liu, Q.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional protein SWT1


Theoretical massNumber of molelcules
Total (without water)19,6461
Polymers19,6461
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.518, 61.518, 84.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcriptional protein SWT1 / Synthetically lethal with TREX protein 1


Mass: 19645.986 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 312-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWT1, YOR166C, O3595 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q12104
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 2 M sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 8495 / Num. obs: 8407 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 61.89
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5.99 / Num. unique all: 420 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET DERIVATIVE OF L379M MUTANT

Resolution: 2.3→28.322 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 394 4.69 %random
Rwork0.2118 ---
all0.2143 8495 --
obs0.2118 8407 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.562 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.7337 Å20 Å2-0 Å2
2---7.7337 Å20 Å2
3---15.4674 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 25 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091180
X-RAY DIFFRACTIONf_angle_d1.1411595
X-RAY DIFFRACTIONf_dihedral_angle_d15.95427
X-RAY DIFFRACTIONf_chiral_restr0.084175
X-RAY DIFFRACTIONf_plane_restr0.004198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.63280.34091240.26712645X-RAY DIFFRACTION98
2.6328-3.31630.29751310.21592717X-RAY DIFFRACTION100
3.3163-28.32450.241390.20052651X-RAY DIFFRACTION93

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