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- PDB-3wfp: tRNA processing enzyme (apo form 2) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3wfp
TitletRNA processing enzyme (apo form 2)
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
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 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
CC-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.005 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_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
D: Poly A polymerase
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)447,39816
Polymers446,6298
Non-polymers7698
Water0
1
A: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9252
Polymers55,8291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Poly A polymerase
B: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8494
Polymers111,6572
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-11 kcal/mol
Surface area41710 Å2
MethodPISA
10
C: Poly A polymerase
D: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8494
Polymers111,6572
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-12 kcal/mol
Surface area36640 Å2
MethodPISA
11
E: Poly A polymerase
F: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8494
Polymers111,6572
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-14 kcal/mol
Surface area35460 Å2
MethodPISA
12
G: Poly A polymerase
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8494
Polymers111,6572
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-11 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.910, 138.360, 147.620
Angle α, β, γ (deg.)90.00, 111.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Poly A polymerase


Mass: 55828.664 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria), (gene. exp.) synthetic construct (others)
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.: 8 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE AUTHORS CRYSTALLIZED THE FRAGMENT PROTEIN, RESIDUES 16-512 FOR ALL CHAINS. THE AUTHORS KNOW THE ...THE AUTHORS CRYSTALLIZED THE FRAGMENT PROTEIN, RESIDUES 16-512 FOR ALL CHAINS. THE AUTHORS KNOW THE COMPLETE SEQUENCE. THE SEQUENCE OF RESIDUES 451-512 (THE UNK PART) IS AS FOLLOWS. (451)IQKPLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTKNLKPLDEG(512) THE AUTHORS COULD OBSERVE A PART OF C-TERMINAL RESIDUES 451-512 OF ONLY CHAIN A AND B. 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: 2.71 Å3/Da / Density % sol: 54.58 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorDate: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. obs: 34980 / Biso Wilson estimate: 68.62 Å2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFO

3wfo


Resolution: 4.005→19.969 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7558 / SU ML: 0.74 / σ(F): 2.01 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3139 1732 5 %
Rwork0.2575 --
obs0.2604 34646 86.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 317.23 Å2 / Biso mean: 142.6656 Å2 / Biso min: 45.77 Å2
Refinement stepCycle: LAST / Resolution: 4.005→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27524 0 40 0 27564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328124
X-RAY DIFFRACTIONf_angle_d0.78137898
X-RAY DIFFRACTIONf_chiral_restr0.0344158
X-RAY DIFFRACTIONf_plane_restr0.0034864
X-RAY DIFFRACTIONf_dihedral_angle_d11.04910564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0051-4.12190.4865190.356936638512
4.1219-4.25370.4213630.31751198126138
4.2537-4.40420.31261390.29692880301991
4.4042-4.57850.37471600.300231613321100
4.5785-4.78410.35051750.285431383313100
4.7841-5.03260.37441590.249331533312100
5.0326-5.34220.30251820.248531673349100
5.3422-5.74550.27881560.254831453301100
5.7455-6.30710.33161850.26131573342100
6.3071-7.18240.32381430.270131893332100
7.1824-8.91310.2821730.23231673340100
8.9131-19.96930.23751780.2013193337199
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)
12.69760.64741.60272.3051-1.46018.64320.2456-0.3795-0.01050.3416-0.03080.2891-0.5209-0.4358-0.20050.7088-0.05770.02530.5013-0.07290.655114.5673-12.2242147.0916
23.15120.88462.10171.7662.96937.6723-0.26940.1553-0.0618-0.25420.2931-0.3422-0.19861.4423-0.04320.8018-0.04160.10020.92690.16650.682242.1703-10.7108126.3367
37.09161.38011.82831.6777-0.09053.74590.1121-0.37790.3081-0.36480.17640.56-0.0838-0.9248-0.23130.96050.1255-0.09231.18030.20640.7752-17.6542-5.144352.7486
45.5936-0.8503-0.19052.0796-1.20356.4748-0.27630.0870.40240.27280.28720.07780.1036-0.2577-0.00450.9106-0.029-0.26821.1373-0.00280.63630.5483-6.330682.1745
52.9492-0.9335-0.31282.44671.11394.64130.2840.13271.04220.02830.03020.3764-1.8025-0.703-0.25261.28740.08970.28990.6321-0.00831.53699.3745-46.6219110.978
62.66350.41262.45582.36242.25126.74290.13860.72-0.0491-0.25480.0912-0.28890.21091.3656-0.26520.86580.15610.30710.7999-0.00950.804633.2751-70.2681104.3517
72.6511.07830.10790.85010.58764.9990.20950.040.11130.23470.2125-0.2532-1.4634-0.3728-0.43121.65640.10030.46790.76850.40472.022-21.2022-45.442166.3195
81.67771.04460.48333.7115-2.93713.55850.02880.1060.09340.65840.64731.1607-0.4415-1.4224-0.68711.1210.04680.47491.7488-0.01311.4193-50.3917-63.6724169.1151
90.44810.7015-0.61681.2921-1.09150.94060.01280.43740.3482-0.39130.38621.4898-1.1408-0.6279-0.18132.27150.0652-1.0438-0.006-0.02281.9202-2.959919.233114.5972
101.17511.8631-0.35342.8716-0.57320.119-0.1393-0.8529-0.48831.18480.054-0.3376-0.4175-0.60750.08791.0530.0045-0.62282.98720.0270.81454.670824.7429159.3679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 17:450)A17 - 450
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 17:450)B17 - 450
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 17:448)C17 - 448
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 17:448)D17 - 448
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 17:448)E17 - 448
6X-RAY DIFFRACTION6CHAIN F AND (RESSEQ 17:448)F17 - 448
7X-RAY DIFFRACTION7CHAIN G AND (RESSEQ 17:448)G17 - 448
8X-RAY DIFFRACTION8CHAIN H AND (RESSEQ 17:448)H17 - 448
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 461:501)A - I461 - 501
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 461:504)B - J461 - 504

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