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- PDB-4oi0: bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition s... -

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Basic information

Entry
Database: PDB / ID: 4oi0
Titlebound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)
Components
  • Protein clpf-1
  • RNA (5'-R(*GP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / polynucleotide kinase / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Processing of Capped Intron-Containing Pre-mRNA / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / mRNA 3'-end processing / ATP binding / nucleus
Similarity search - Function
Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain / Clp1, C-terminal domain superfamily / Clp1, N-terminal beta-sandwich domain superfamily / Pre-mRNA cleavage complex II protein Clp1 / N-terminal beta-sandwich domain of polyadenylation factor / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain ...Pre-mRNA cleavage complex subunit Clp1, C-terminal domain / Clp1, DNA binding domain / Pre-mRNA cleavage complex subunit Clp1, C-terminal / Polyribonucleotide 5-hydroxyl-kinase Clp1 / Clp1, N-terminal beta-sandwich domain / Clp1, C-terminal domain superfamily / Clp1, N-terminal beta-sandwich domain superfamily / Pre-mRNA cleavage complex II protein Clp1 / N-terminal beta-sandwich domain of polyadenylation factor / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Jelly Rolls / Beta Barrel / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / SARCOSINE / RNA / Protein clpf-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsDikfidan, A. / Loll, B. / Zeymer, C. / Clausen, T. / Meinhart, A.
CitationJournal: Mol.Cell / Year: 2014
Title: RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Authors: Dikfidan, A. / Loll, B. / Zeymer, C. / Magler, I. / Clausen, T. / Meinhart, A.
History
DepositionJan 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Protein clpf-1
B: RNA (5'-R(*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6898
Polymers48,5422
Non-polymers1,1476
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.710, 100.710, 40.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Protein clpf-1


Mass: 47936.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: clpf-1, F59A2.4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P52874
#2: RNA chain RNA (5'-R(*GP*C)-3')


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized

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Non-polymers , 6 types, 141 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-SAR / SARCOSINE


Type: peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Description: Diffraction data include Deby-Scherrer rings at 3.62 Angstrom and 2.25 Angstrom resolution from salt in the cryo solution
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na2HPO4/KH2PO4 200 mM NaCl 15 mM MgCl2 90 mM sarcosine 25% (w/v) PEG 1000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2010 / Details: Rigaku VariMax
RadiationMonochromator: OSMIC KB MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22553 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 36.8 Å2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / % possible all: 83.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→36.66 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.481 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 1108 5 %RANDOM
Rwork0.22677 ---
obs0.22938 21145 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 40 58 135 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223331
X-RAY DIFFRACTIONr_bond_other_d0.0010.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9994534
X-RAY DIFFRACTIONr_angle_other_deg0.79235514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60724.406143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
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_it0.4121.52022
X-RAY DIFFRACTIONr_mcbond_other0.0831.5824
X-RAY DIFFRACTIONr_mcangle_it0.77923290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.20331309
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9894.51231
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.577 62 -
Rwork0.562 1223 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.8994-0.8433-1.36951.5016-0.37092.3553-0.2834-0.04520.27180.15550.15320.0050.05120.04970.13020.19350.05570.02260.02840.01320.0249-2.597515.0663-4.5305
21.2145-0.5399-0.24813.14380.32392.17610.02380.00760.14140.0688-0.04560.0642-0.1421-0.22790.02180.09460.02290.0290.0865-0.00980.0471-18.13325.72825.0976
34.19920.62240.17896.52640.21194.5438-0.1119-0.15660.6506-0.02270.16110.2428-0.448-0.2357-0.04920.24490.06360.03240.0719-0.01310.3189-14.911951.72386.1949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 106
2X-RAY DIFFRACTION2A111 - 310
3X-RAY DIFFRACTION3A311 - 423

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