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- PDB-3els: Crystal Structure of Yeast Pml1p, Residues 51-204 -

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Basic information

Entry
Database: PDB / ID: 3els
TitleCrystal Structure of Yeast Pml1p, Residues 51-204
ComponentsPre-mRNA leakage protein 1
KeywordsSPLICING / Intrinsically unstructured domain / forkhead-associated domain (FHA) domain / pre-mRNA retention and splicing / protein phosphorylation / RES complex / mRNA processing / mRNA splicing / Nucleus
Function / homology
Function and homology information


maintenance of RNA location / RES complex / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / nucleus / cytoplasm
Similarity search - Function
: / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre-mRNA leakage protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTrowitzsch, S. / Weber, G. / Luehrmann, R. / Wahl, M.C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex.
Authors: Trowitzsch, S. / Weber, G. / Luhrmann, R. / Wahl, M.C.
History
DepositionSep 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA leakage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4787
Polymers18,0501
Non-polymers4286
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Pre-mRNA leakage protein 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)110,87142
Polymers108,3026
Non-polymers2,56936
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area19520 Å2
ΔGint-87 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.613, 100.613, 102.196
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1-

MG

21A-205-

CL

31A-295-

HOH

41A-296-

HOH

51A-340-

HOH

61A-357-

HOH

71A-368-

HOH

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Components

#1: Protein Pre-mRNA leakage protein 1


Mass: 18050.314 Da / Num. of mol.: 1 / Fragment: UNP residues 51 to 204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PML1, YLR016C, L1591 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q07930
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCl, pH 7.5, 200 mM Li2SO4, 21-24 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9802 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 1.8→40.7 Å / Num. obs: 16896 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 71.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2473 / Rsym value: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.859 / SU ML: 0.089 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23611 949 5.1 %RANDOM
Rwork0.18898 ---
all0.19133 17744 --
obs0.19133 17665 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.309 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0.84 Å20 Å2
2---1.69 Å20 Å2
3---2.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 26 185 1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221262
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9841708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65323.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92515227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6721512
X-RAY DIFFRACTIONr_chiral_restr0.090.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02961
X-RAY DIFFRACTIONr_nbd_refined0.1990.2534
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2848
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2152
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.243
X-RAY DIFFRACTIONr_mcbond_it0.8261.5777
X-RAY DIFFRACTIONr_mcangle_it1.30821229
X-RAY DIFFRACTIONr_scbond_it1.8593547
X-RAY DIFFRACTIONr_scangle_it2.9174.5476
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 69 -
Rwork0.265 1258 -
obs--98.52 %

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