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- PDB-3wfs: tRNA processing enzyme complex 3 -

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Basic information

Entry
Database: PDB / ID: 3wfs
TitletRNA processing enzyme complex 3
Components
  • Poly A polymerase
  • RNA (74-MER)
KeywordsTransferase/RNA / Terminal Nucleotide Transferase / Transferase-RNA complex
Function / homology
Function and homology information


CTP:tRNA cytidylyltransferase activity / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / nucleotide binding / metal ion binding
Similarity search - Function
: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. ...: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / CC-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciessynthetic construct (others)
Aquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.311 Å
AuthorsYamashita, S. / Takeshita, D. / Tomita, K.
CitationJournal: Structure / Year: 2014
Title: Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase
Authors: Yamashita, S. / Takeshita, D. / Tomita, K.
History
DepositionJul 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RNA (74-MER)
B: RNA (74-MER)
C: Poly A polymerase
D: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9718
Polymers161,5864
Non-polymers3844
Water00
1
A: RNA (74-MER)
C: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9854
Polymers80,7932
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-41 kcal/mol
Surface area32630 Å2
MethodPISA
2
B: RNA (74-MER)
D: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9854
Polymers80,7932
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-43 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.210, 148.110, 92.250
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (74-MER)


Mass: 23850.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 498539165
#2: Protein Poly A polymerase


Mass: 56943.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: pcnB2 / Production host: Escherichia coli (E. coli)
References: UniProt: O67911, CCA tRNA nucleotidyltransferase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR C, D CHAINS. THE AUTHORS KNOW THE ...THE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR C, D CHAINS. THE AUTHORS KNOW THE COMPLETE SEQUENCE. THE SEQUENCE OF RESIDUES 1-15 AND 449-512 (THE UNK PART) IS AS FOLLOWS. (1) MENIEIVSSGKHTLH (15), (449) EEIQKPLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTKNLKPLDEG(512) THE AUTHORS COULD OBSERVE A PART OF N- and C-TERMINAL RESIDUES (1-15 and 449-512, RESPECTIVLY) OF ALL PROTEIN CHAINS BUT THEY ARE NOT SURE WHICH PART CORRESPONDS WITH THESE OBSERVED RESIDUES. SO THE RESIDUE NUMBERS OF UNK ARE MEANINGLESS.

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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: 3.69 Å3/Da / Density % sol: 66.63 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorDate: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 27238 / Biso Wilson estimate: 62.78 Å2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFO, 3L0U

3wfo

3l0u


Resolution: 3.311→19.861 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8072 / SU ML: 0.41 / σ(F): 1.99 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1363 5.02 %
Rwork0.2287 --
obs0.2311 27165 77.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 342.19 Å2 / Biso mean: 113.7954 Å2 / Biso min: 17.81 Å2
Refinement stepCycle: LAST / Resolution: 3.311→19.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7021 3130 20 0 10171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510668
X-RAY DIFFRACTIONf_angle_d0.71815118
X-RAY DIFFRACTIONf_chiral_restr0.0341806
X-RAY DIFFRACTIONf_plane_restr0.0031385
X-RAY DIFFRACTIONf_dihedral_angle_d13.0734413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3113-3.4290.2486210.25432602818
3.429-3.56560.3572520.263184289426
3.5656-3.72690.27661050.26271948205359
3.7269-3.92190.31231450.25312926307189
3.9219-4.16550.2661680.232933083476100
4.1655-4.48370.28371830.220733313514100
4.4837-4.92870.26251580.222233283486100
4.9287-5.62760.27491830.222533043487100
5.6276-7.03740.30511670.247733563523100
7.0374-19.8610.24481810.20113199338095
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)
11.5751-1.6169-0.27013.42211.85951.3868-0.2549-0.3620.0101-0.69330.3563-0.28451.32191.3758-0.14641.81330.41470.24831.26660.01210.661755.07775.1691-29.1272
21.689-0.4779-0.94611.85631.11380.99190.0025-0.97780.53570.88040.9363-0.2422-0.97691.7028-0.50241.8999-0.02750.13861.3179-0.17340.49451.83139.389932.8088
32.2492-0.2595-0.56884.2624-0.34582.9884-0.31820.1944-0.16360.9399-0.05620.28420.3008-0.07270.16020.33-0.03760.09130.1804-0.06640.497737.397225.9476-2.3673
42.3444-3.1237-0.39564.53741.05120.7971-0.1171-0.14920.91850.0878-0.106-0.3246-0.13280.18110.19911.1336-0.44210.43963.276-1.1152.835179.622233.7942-28.9418
51.9164-0.5875-0.81674.71280.38732.62860.7149-0.22820.4415-1.4635-0.0386-0.9085-1.01070.94530.30370.3737-0.0653-0.00470.37830.14660.239356.7853-14.10183.9113
63.5194-1.23112.61117.6083-2.51197.46060.4554-0.0378-0.5074-0.1119-0.1615-0.1921-0.15920.1539-0.07921.26960.4927-0.55561.7890.19450.894272.4781-17.479349.0855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:74)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:74)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 5:448 OR RESSEQ 1001:1002)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 473:504)
5X-RAY DIFFRACTION5CHAIN D AND (RESSEQ 5:448 OR RESSEQ 1001:1002)
6X-RAY DIFFRACTION6CHAIN D AND (RESSEQ 473:504)

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