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- PDB-8px5: Structure of the RNA recognition motif (RRM) of Seb1 from S. pomb... -

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Basic information

Entry
Database: PDB / ID: 8px5
TitleStructure of the RNA recognition motif (RRM) of Seb1 from S. pombe., solved at wavelength 2.75 A
ComponentsRpb7-binding protein seb1
KeywordsTRANSCRIPTION / RRM / RNA binding protein
Function / homology
Function and homology information


Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / regulatory ncRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / pericentric heterochromatin formation / chromatin-protein adaptor activity / mRNA 3'-end processing / termination of RNA polymerase II transcription / snoRNA binding / lncRNA binding ...Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / regulatory ncRNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / pericentric heterochromatin formation / chromatin-protein adaptor activity / mRNA 3'-end processing / termination of RNA polymerase II transcription / snoRNA binding / lncRNA binding / RNA polymerase II C-terminal domain binding / molecular condensate scaffold activity / RNA binding / nucleus
Similarity search - Function
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Rpb7-binding protein seb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Wittmann, S. / Renner, M. / Grimes, J.M. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rpb7-binding protein seb1


Theoretical massNumber of molelcules
Total (without water)17,3781
Polymers17,3781
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.100, 46.900, 32.300
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rpb7-binding protein seb1


Mass: 17377.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: seb1, SPAC222.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M ammonium formate, 100 mM sodium cacodylate, 8% (w/v) poly-gamma-glutamic acid polymer (PGA-LM, 200-400 kDa low molecular weight polymer)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.775→54.87 Å / Num. obs: 10445 / % possible obs: 64.89 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04513 / Rpim(I) all: 0.01897 / Rrim(I) all: 0.04915 / Net I/σ(I): 22.91
Reflection shellResolution: 1.775→1.838 Å / Rmerge(I) obs: 0.2519 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 653 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→54.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.928 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18829 545 5.2 %RANDOM
Rwork0.15472 ---
obs0.15652 9850 64.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å20.61 Å2
2--1.63 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.77→54.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 0 85 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171158
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.6551651
X-RAY DIFFRACTIONr_angle_other_deg1.0861.5762668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0285151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.52218.98669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.915203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0751515
X-RAY DIFFRACTIONr_chiral_restr0.0620.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.021368
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4352.161607
X-RAY DIFFRACTIONr_mcbond_other2.4162.155606
X-RAY DIFFRACTIONr_mcangle_it3.2543.23757
X-RAY DIFFRACTIONr_mcangle_other3.2523.236758
X-RAY DIFFRACTIONr_scbond_it3.3082.524612
X-RAY DIFFRACTIONr_scbond_other3.2582.525612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6673.657895
X-RAY DIFFRACTIONr_long_range_B_refined5.63725.7971333
X-RAY DIFFRACTIONr_long_range_B_other5.59825.7031324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.775→1.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 16 -
Rwork0.225 434 -
obs--38.66 %

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