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- PDB-5r4u: PanDDA analysis group deposition -- Crystal Structure of HUMAN CL... -

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Basic information

Entry
Database: PDB / ID: 5r4u
TitlePanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with EN08775-43
ComponentsCleavage and polyadenylation specificity factor subunit 5
KeywordsRNA BINDING PROTEIN / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer / CPSF5 / RNA PROCESSING / CLEAVAGE FACTOR / MRNA PROCESSING / NUCLEUS / PHOSPHOPROTEIN / RNA-BINDING
Function / homology
Function and homology information


positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / protein heterotetramerization / post-transcriptional regulation of gene expression / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / protein tetramerization / histone deacetylase binding / mRNA processing / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-RWM / Cleavage and polyadenylation specificity factor subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.92 Å
AuthorsKidd, S.L. / Mateu, N. / Talon, R. / Krojer, T. / Aimon, A. / Bradley, A.R. / Fairhead, M. / Diaz-Saez, L. / Sore, H.F. / Madin, A. ...Kidd, S.L. / Mateu, N. / Talon, R. / Krojer, T. / Aimon, A. / Bradley, A.R. / Fairhead, M. / Diaz-Saez, L. / Sore, H.F. / Madin, A. / Huber, K.V.M. / von Delft, F. / Spring, D.R.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Kidd, S.L. / Mateu, N. / Talon, R. / Krojer, T. / Aimon, A. / Bradley, A.R. / Fairhead, M. / Diaz-Saez, L. / Sore, H.F. / Madin, A. / Huber, K.V.M. / von Delft, F. / Spring, D.R.
History
DepositionFeb 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58912
Polymers45,7492
Non-polymers84010
Water4,576254
1
A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules

A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,78712
Polymers45,7492
Non-polymers1,03810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4120 Å2
ΔGint-223 kcal/mol
Surface area17990 Å2
MethodPISA
2
B: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules

B: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,39012
Polymers45,7492
Non-polymers64110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3520 Å2
ΔGint-128 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.060, 59.060, 212.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Cleavage ...Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Cleavage factor Im complex 25 kDa subunit / CFIm25 / Nucleoside diphosphate-linked moiety X motif 21 / Nudix motif 21 / Nudix hydrolase 21 / Pre-mRNA cleavage factor Im 68 kDa subunit


Mass: 22874.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O43809
#2: Chemical ChemComp-RWM / (5S)-5-methyl-5-[(3-phenyl-1,2-oxazol-5-yl)methyl]pyrrolidine-2,4-dione


Mass: 270.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.17 Å3/Da / Density % sol: 43.43 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1 / Details: 0.1M acetate pH 5.1, 0.0025M ZnAC, 6% PEG3K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.92→49.73 Å / Num. obs: 33630 / % possible obs: 98.8 % / Redundancy: 9.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.067 / Rrim(I) all: 0.2 / Net I/σ(I): 10.3 / Num. measured all: 310501 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.978.87.382094423750.3952.6487.8570.695.2
8.59-49.738.20.05837844630.9970.0220.06333.499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3BAP

3bap


Resolution: 1.92→49.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.652 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 1684 5 %RANDOM
Rwork0.2136 ---
obs0.2162 31864 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.08 Å2 / Biso mean: 31.716 Å2 / Biso min: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: final / Resolution: 1.92→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 38 254 3452
Biso mean--60.7 39.91 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133888
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173347
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6725018
X-RAY DIFFRACTIONr_angle_other_deg1.2571.5827794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9785461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97722.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43115609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6431523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024376
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02797
X-RAY DIFFRACTIONr_mcbond_it2.8263.2641861
X-RAY DIFFRACTIONr_mcbond_other2.8223.261853
X-RAY DIFFRACTIONr_mcangle_it4.534.892245
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 118 -
Rwork0.409 2247 -
all-2365 -
obs--94.83 %

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