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- PDB-4q2s: Crystal Structure of S. pombe Pdc1 Ge1 Domain -

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Basic information

Entry
Database: PDB / ID: 4q2s
TitleCrystal Structure of S. pombe Pdc1 Ge1 Domain
ComponentsPDC1 GE1 DOMAIN
KeywordsRNA BINDING PROTEIN / Ge1 domain / P-body assembly
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / P-body assembly / P-body / molecular condensate scaffold activity / cytoplasmic stress granule / molecular adaptor activity / cytoplasm
Similarity search - Function
: / Pdc1 Ge1 domain / Enhancer of mRNA-decapping protein 4-like / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 4-like protein pdc1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / after obtaining initial molecular replacement model by S-SAD / Resolution: 1.35 Å
AuthorsNoeldeke, E.R. / Neu, A. / Zocher, G. / Sprangers, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery.
Authors: Fromm, S.A. / Kamenz, J. / Noldeke, E.R. / Neu, A. / Zocher, G. / Sprangers, R.
History
DepositionApr 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDC1 GE1 DOMAIN


Theoretical massNumber of molelcules
Total (without water)16,2421
Polymers16,2421
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.330, 77.840, 36.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PDC1 GE1 DOMAIN / UNCHARACTERIZED PROTEIN C20G4.08


Mass: 16241.898 Da / Num. of mol.: 1 / Fragment: unp residues 932-1070
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC20G4.08, SPAC4F10.01 / Production host: Escherichia coli (E. coli) / References: UniProt: O13892
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Acetate, 0.1 M HEPES, 25% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40.4 Å / Num. all: 30393 / Num. obs: 30287 / % possible obs: 99.7 % / Observed criterion σ(I): -2
Reflection shellResolution: 1.35→1.39 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: after obtaining initial molecular replacement model by S-SAD
Resolution: 1.35→40.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.516 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21164 2120 7 %RANDOM
Rwork0.18476 ---
obs0.18675 28166 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å20 Å2
2--0.39 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 0 70 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191112
X-RAY DIFFRACTIONr_bond_other_d0.0010.021089
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9841513
X-RAY DIFFRACTIONr_angle_other_deg0.84132497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7495143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56922.76647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1521511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_mcbond_it2.3431.793557
X-RAY DIFFRACTIONr_mcbond_other2.3351.791556
X-RAY DIFFRACTIONr_mcangle_it2.762.705699
X-RAY DIFFRACTIONr_mcangle_other2.7612.707700
X-RAY DIFFRACTIONr_scbond_it2.9582.089555
X-RAY DIFFRACTIONr_scbond_other2.952.081552
X-RAY DIFFRACTIONr_scangle_other3.6433.014812
X-RAY DIFFRACTIONr_long_range_B_refined3.86215.351375
X-RAY DIFFRACTIONr_long_range_B_other3.76215.1161350
X-RAY DIFFRACTIONr_rigid_bond_restr2.58732201
X-RAY DIFFRACTIONr_sphericity_free32.778523
X-RAY DIFFRACTIONr_sphericity_bonded14.152228
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 154 -
Rwork0.29 2056 -
obs--99.95 %

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