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- PDB-3wfr: tRNA processing enzyme complex 2 -

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Basic information

Entry
Database: PDB / ID: 3wfr
TitletRNA processing enzyme complex 2
Components
  • Poly A polymerase
  • RNA (74-MER)
  • RNA (75-MER)
KeywordsTransferase/RNA / Terminal Nucleotide Transferase / Transferase-RNA complex
Function / homology
Function and homology information


CTP:tRNA cytidylyltransferase activity / RNA 3'-end processing / 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. / HD/PDEase domain ...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
CYTIDINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / : / 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: 3.501 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: RNA (75-MER)
D: RNA (75-MER)
E: Poly A polymerase
F: Poly A polymerase
G: Poly A polymerase
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,33020
Polymers324,5968
Non-polymers2,73412
Water00
1
A: RNA (74-MER)
E: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6805
Polymers80,9962
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (74-MER)
F: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6805
Polymers80,9962
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (75-MER)
G: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9855
Polymers81,3022
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (75-MER)
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9855
Polymers81,3022
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.810, 154.590, 174.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F
32chain G
42chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCBCchain AAA1 - 741 - 74
21GGCBCchain BBB1 - 741 - 74
31GGCBCchain CCC1 - 751 - 75
41GGCBCchain DDD1 - 751 - 75
12UNKUNKUNKUNKchain EEE5 - 5055 - 505
22UNKUNKUNKUNKchain FFF5 - 5055 - 505
32UNKUNKUNKUNKchain GGG5 - 5055 - 505
42UNKUNKUNKUNKchain HHH5 - 5055 - 505

NCS ensembles :
ID
1
2

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Components

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RNA chain , 2 types, 4 molecules ABCD

#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: RNA chain RNA (75-MER)


Mass: 24155.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 498539165

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Protein , 1 types, 4 molecules EFGH

#3: Protein
Poly A polymerase


Mass: 57146.211 Da / Num. of mol.: 4
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

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Details

Sequence detailsTHE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW ...THE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW THE COMPLETE SEQUENCE. THE SEQUENCE OF RESIDUES 1-15 AND 454-512 (THE UNK PART) IS AS FOLLOWS. (1) MENIEIVSSGKHTLH (15), (454)PLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTKNLKPLDEG(512) THE AUTHORS COULD OBSERVE A PART OF N- and C-TERMINAL RESIDUES (1-15 and 454-512, 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

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorDate: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 37144 / Biso Wilson estimate: 19.43 Å2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFO, 3L0U

3wfo

3l0u


Resolution: 3.501→19.975 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8229 / SU ML: 0.45 / σ(F): 2 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1839 4.99 %RANDOM
Rwork0.2244 ---
obs0.2267 36827 70.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 441.49 Å2 / Biso mean: 128.5234 Å2 / Biso min: 33.62 Å2
Refinement stepCycle: LAST / Resolution: 3.501→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14291 6300 156 0 20747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621843
X-RAY DIFFRACTIONf_angle_d0.73330981
X-RAY DIFFRACTIONf_chiral_restr0.0463703
X-RAY DIFFRACTIONf_plane_restr0.0032829
X-RAY DIFFRACTIONf_dihedral_angle_d12.5879031
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3544X-RAY DIFFRACTION10.526TORSIONAL
12B3544X-RAY DIFFRACTION10.526TORSIONAL
13C3544X-RAY DIFFRACTION10.526TORSIONAL
14D3544X-RAY DIFFRACTION10.526TORSIONAL
21E8069X-RAY DIFFRACTION10.526TORSIONAL
22F8069X-RAY DIFFRACTION10.526TORSIONAL
23G8069X-RAY DIFFRACTION10.526TORSIONAL
24H8069X-RAY DIFFRACTION10.526TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.501-3.59520.3254390.314159062916
3.5952-3.70030.3066550.27391094114929
3.7003-3.8190.3194610.24961481154239
3.819-3.95440.2707910.22971803189447
3.9544-4.11140.27251030.23122126222956
4.1114-4.29680.27021370.2242466260365
4.2968-4.52090.26071470.22432836298375
4.5209-4.80040.25941720.21523272344486
4.8004-5.16510.29372250.20583703392897
5.1651-5.67410.27072030.221538264029100
5.6741-6.47060.30061870.237138914078100
6.4706-8.06210.25342020.22539034105100
8.0621-19.97560.2162170.202639974214100
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)
15.1645-1.1265-1.90261.94590.12391.2452-0.3645-1.7669-0.22371.7590.02210.9113-0.3388-0.88290.36091.71770.01710.4292.2779-0.04241.27349.316148.4383-13.055
23.59-0.0467-1.11891.96430.65830.9042-0.4876-2.1861-0.21531.25180.0433-0.59951.09851.05910.40042.01980.1099-0.2852.37540.02451.114887.392937.6002-17.1843
35.2128-1.4916-2.50170.67170.2831.85610.1241-2.28960.98281.56-0.31860.4648-0.5212-0.18640.16132.2183-0.29580.57292.0951-0.48281.4471-7.2239-14.3024-8.2646
45.6038-0.06032.09182.10531.45781.8437-0.0763-2.80250.1172.0099-0.0438-1.359-0.81871.25420.1572.4151-0.5901-0.74062.73790.07281.740364.1754-14.4353-8.0889
52.5287-0.47990.18665.39451.21221.3845-0.0293-0.110.4319-0.26-0.2487-0.0508-0.3626-0.09710.3170.4255-0.0397-0.0130.6110.03420.354630.625151.4349-42.8607
64.97380.49290.80171.4684-0.16810.1722-0.31040.0120.7755-0.3419-0.51650.0864-0.8802-0.74220.81193.2409-0.3633-0.28562.1424-0.8561.711333.683570.61442.9566
73.1629-1.1273-0.36434.81441.09581.29050.16540.08910.6524-0.1613-0.1248-0.6134-0.28690.1553-0.01160.453-0.12970.02120.66380.10440.575565.363550.9889-43.6341
81.4010.2409-1.12811.0332-0.14852.26040.09670.7122-0.2197-0.9281-0.4277-0.13960.15130.32220.33712.68-0.4253-0.07961.29110.07141.166763.81239.556-15.7521
93.64411.06030.10795.5148-0.07911.2173-0.04190.2252-0.00670.1139-0.12840.54570.0286-0.11610.16070.3656-0.14610.08950.7236-0.04520.525210.7753-25.1416-42.1367
102.3628-1.5165-0.36124.66042.55291.5186-0.8043-1.0158-0.03582.2258-0.32540.29690.1924-0.66111.11662.4615-0.08220.21761.1447-0.4811.555314.083815.8954-13.7988
112.69270.1943-0.43873.8509-1.66481.74280.0419-0.0349-0.1628-0.28290.03020.02430.30790.001-0.07920.3548-0.0649-0.13640.5298-0.09580.431645.7902-24.2004-41.7717
120.13610.06430.29790.04240.13480.649-0.0226-0.1558-0.06840.2660.02320.07690.1014-0.01180.00372.0882-0.04570.11761.76950.58520.855242.2559-40.86734.4969
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 1:75)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 1:75)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 5:448)
6X-RAY DIFFRACTION6CHAIN E AND (RESSEQ 473:505)
7X-RAY DIFFRACTION7CHAIN F AND (RESSEQ 5:448)
8X-RAY DIFFRACTION8CHAIN F AND (RESSEQ 473:505)
9X-RAY DIFFRACTION9CHAIN G AND (RESSEQ 5:450)
10X-RAY DIFFRACTION10CHAIN G AND (RESSEQ 461:505)
11X-RAY DIFFRACTION11CHAIN H AND (RESSEQ 5:453)
12X-RAY DIFFRACTION12CHAIN H AND (RESSEQ 461:505)

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