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- PDB-4oi2: C. Elegans Clp1 and ADP and Mg2+ (turnover state) -

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Basic information

Entry
Database: PDB / ID: 4oi2
TitleC. Elegans Clp1 and ADP and Mg2+ (turnover state)
ComponentsProtein clpf-1
KeywordsRNA BINDING PROTEIN / polynucleotide kinase
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 / Protein clpf-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8024
Polymers47,9361
Non-polymers8663
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.150, 100.150, 40.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#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: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 49.61 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 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: 2.6→50 Å / Num. obs: 13457 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 54 Å2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.1 % / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→32.77 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 23.356 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25558 668 5 %RANDOM
Rwork0.20266 ---
obs0.20525 12787 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 41 54 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223226
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8721.9774369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5845401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20724.326141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67515565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3981519
X-RAY DIFFRACTIONr_chiral_restr0.0540.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022381
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1560.21299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22179
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.211.52053
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.36823225
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.34731323
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5824.51141
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 55 -
Rwork0.287 997 -
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)
18.1143-0.27070.05071.5665-0.2461.7835-0.11020.10850.14880.06410.0758-0.015-0.0450.110.03440.03060.03710.0471-0.1345-0.0084-0.1233-2.329915.0673-4.6778
21.7426-0.4926-0.49933.1918-0.08681.83890.0858-0.01770.17470.08870.00910.0265-0.1134-0.0889-0.0949-0.05190.02070.0365-0.0567-0.0135-0.091-18.319425.57155.0365
35.24721.15050.55226.02330.13254.6281-0.2347-0.18320.5833-0.00080.26010.2983-0.4946-0.0605-0.0254-0.05850.06080.0112-0.25-0.0080.0293-14.946651.25896.5718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 105
2X-RAY DIFFRACTION2A111 - 310
3X-RAY DIFFRACTION3A311 - 423

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