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- PDB-1vfg: Crystal structure of tRNA nucleotidyltransferase complexed with a... -

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Basic information

Entry
Database: PDB / ID: 1vfg
TitleCrystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
Components
  • RNA (75-MER)
  • poly A polymerase
KeywordsTRANSFERASE/RNA / TRANSFERASE / RNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / RNA 3'-end processing / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain ...cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / Poly A polymerase, head domain / Poly A polymerase head domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / RNA / RNA (> 10) / A-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTomita, K. / Fukai, S. / Ishitani, R. / Ueda, T. / Takeuchi, N. / Vassylyev, D.G. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nature / Year: 2004
Title: Structural basis for template-independent RNA polymerization.
Authors: Tomita, K. / Fukai, S. / Ishitani, R. / Ueda, T. / Takeuchi, N. / Vassylyev, D.G. / Nureki, O.
History
DepositionApr 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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
C: RNA (75-MER)
D: RNA (75-MER)
A: poly A polymerase
B: poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7656
Polymers139,7544
Non-polymers1,0102
Water1,42379
1
C: RNA (75-MER)
A: poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3823
Polymers69,8772
Non-polymers5051
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA (75-MER)
B: poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3823
Polymers69,8772
Non-polymers5051
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.476, 125.900, 58.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: RNA chain RNA (75-MER)


Mass: 24155.350 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA Polymerase in Thermotoga maritima
#2: Protein poly A polymerase / A-adding enzyme


Mass: 45721.840 Da / Num. of mol.: 2 / Fragment: residues 1-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O66728, polynucleotide adenylyltransferase
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 4.1 Å3/Da / Density % sol: 70 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, magnesium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium acetate11
3MPD12
4magnesium acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.000, 0.9793, 0.9795, 0.9843, 0.9743
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 9, 2003 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
30.97951
40.98431
50.97431
ReflectionResolution: 2.8→50 Å / Num. all: 39382 / Num. obs: 39382 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.067 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.398 / % possible all: 95.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This crystal has a pseudo-merohedral perfect twinning in P2, which pretends P2(1)2(1)2. beta is 90 degree since Depositors processed the data with P2(1)2(1)2, and expanded them to the P2 ...Details: This crystal has a pseudo-merohedral perfect twinning in P2, which pretends P2(1)2(1)2. beta is 90 degree since Depositors processed the data with P2(1)2(1)2, and expanded them to the P2 space group. The file contains Friedel pairs.
RfactorNum. reflectionSelection details
Rfree0.2865 1945 RANDOM
Rwork0.2297 --
all-39038 -
obs-39038 -
Displacement parametersBiso mean: 87.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 1384 62 79 7319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.23
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3263 180 -
Rwork0.3013 --
obs--95 %

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