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- PDB-3wfo: tRNA processing enzyme (apo form 1) -

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Basic information

Entry
Database: PDB / ID: 3wfo
TitletRNA processing enzyme (apo form 1)
ComponentsPoly A polymerase
KeywordsTRANSFERASE / Terminal Nucleotide Transferase
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
HDIG domain / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / 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 ...HDIG domain / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / 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
CC-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Poly A polymerase
B: Poly A polymerase
C: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,65514
Polymers181,5983
Non-polymers1,05711
Water0
1
A: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9175
Polymers60,5331
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9175
Polymers60,5331
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8214
Polymers60,5331
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.481, 327.769, 78.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments: (Selection details: chain 'C' RESTRAINED TORSIONS: 6053 Histogram of differences under limit:...)

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Components

#1: Protein Poly A polymerase


Mass: 60532.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: pcnB2 / Production host: Escherichia coli (E. coli)
References: UniProt: O67911, CCA tRNA nucleotidyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4

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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: 3.13 Å3/Da / Density % sol: 60.67 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorDate: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 31733 / Biso Wilson estimate: 108.7 Å2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.4→19.878 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8471 / SU ML: 0.41 / σ(F): 1.33 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 1586 5 %
Rwork0.1797 30118 -
obs0.1813 31704 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 259.34 Å2 / Biso mean: 119.3384 Å2 / Biso min: 52.53 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10415 0 55 0 10470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410677
X-RAY DIFFRACTIONf_angle_d0.81314392
X-RAY DIFFRACTIONf_chiral_restr0.0331572
X-RAY DIFFRACTIONf_plane_restr0.0041840
X-RAY DIFFRACTIONf_dihedral_angle_d12.6334007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4001-3.50920.34471400.329926562796
3.5092-3.63390.32691420.265927142856
3.6339-3.77850.31351420.229326982840
3.7785-3.94920.21951440.18627172861
3.9492-4.15560.19591420.169827152857
4.1556-4.41330.20461440.153627222866
4.4133-4.74970.16591430.150327232866
4.7497-5.21990.18721450.153227522897
5.2199-5.95730.23431450.184927622907
5.9573-7.43960.22681460.200427792925
7.4396-19.87870.16681530.157428803033
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)
15.0869-0.6693-1.1061.06080.43911.5895-0.1559-0.8917-0.05610.26270.2422-0.0410.22190.2988-0.08990.63070.08960.03050.91290.09690.54821.67274.676894.604
21.27850.94570.18555.89271.51641.1076-0.0860.30260.1653-1.3024-0.10120.4032-0.5485-0.05430.15831.07-0.0595-0.18950.70470.03550.7082-30.8551126.49389.796
33.2761-2.17790.27845.27-0.74031.56830.14220.3667-0.0293-0.8233-0.3373-0.08280.27750.26170.20261.040.05560.08250.68960.09380.656328.5059127.679111.3365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:448 OR RESID 601:604 ) )A3 - 448
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:448 OR RESID 601:604 ) )A601 - 604
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 2:449 OR RESID 601:604 ) )B2 - 449
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 2:449 OR RESID 601:604 ) )B601 - 604
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:447 OR RESID 601:603 ) )C3 - 447
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:447 OR RESID 601:603 ) )C601 - 603

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