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- PDB-3u02: Crystal Structure of the tRNA modifier TiaS from Pyrococcus furio... -

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Basic information

Entry
Database: PDB / ID: 3u02
TitleCrystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR225
ComponentsPutative transcription-associated protein TFIIS
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


tRNAIle2-agmatinylcytidine synthase / tRNA wobble cytosine modification / ligase activity, forming carbon-nitrogen bonds / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #2200 / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 - #20 / Domain of unknown function DUF1743 / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / Domain of unknown function (DUF1743) / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold ...Alpha-Beta Plaits - #2200 / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 - #20 / Domain of unknown function DUF1743 / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / Domain of unknown function (DUF1743) / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / CITRIC ACID / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.399 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the tRNA modifier TiaS from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR225
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcription-associated protein TFIIS
B: Putative transcription-associated protein TFIIS
C: Putative transcription-associated protein TFIIS
D: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,58123
Polymers117,4044
Non-polymers2,17719
Water4,864270
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18350 Å2
ΔGint-301 kcal/mol
Surface area37740 Å2
MethodPISA
2
A: Putative transcription-associated protein TFIIS
B: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,14614
Polymers58,7022
Non-polymers1,44412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-162 kcal/mol
Surface area22880 Å2
MethodPISA
3
C: Putative transcription-associated protein TFIIS
D: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4359
Polymers58,7022
Non-polymers7327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-95 kcal/mol
Surface area21580 Å2
MethodPISA
4
A: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1237
Polymers29,3511
Non-polymers7726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0247
Polymers29,3511
Non-polymers6726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6034
Polymers29,3511
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Putative transcription-associated protein TFIIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8315
Polymers29,3511
Non-polymers4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.147, 135.805, 77.269
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer,32.5 kD,82.8%

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative transcription-associated protein TFIIS


Mass: 29351.061 Da / Num. of mol.: 4 / Fragment: Residues 1-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1855 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + magic / References: UniProt: Q8TZX0

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Non-polymers , 5 types, 289 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: Ammonium Sulfate 0.8M, Citric Acid 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 96855 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.399→43.898 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.68 / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 2474 5.06 %
Rwork0.1793 --
obs0.1824 48926 99.5 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.702 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3608 Å2-0 Å21.7456 Å2
2---3.8898 Å20 Å2
3----0.4709 Å2
Refinement stepCycle: LAST / Resolution: 2.399→43.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 0 125 270 8027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087928
X-RAY DIFFRACTIONf_angle_d1.09410725
X-RAY DIFFRACTIONf_dihedral_angle_d17.1053002
X-RAY DIFFRACTIONf_chiral_restr0.0711178
X-RAY DIFFRACTIONf_plane_restr0.0051338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3992-2.44540.3011200.23532495X-RAY DIFFRACTION96
2.4454-2.49530.2671250.20742558X-RAY DIFFRACTION99
2.4953-2.54950.27961400.19112599X-RAY DIFFRACTION100
2.5495-2.60880.28391550.20942523X-RAY DIFFRACTION99
2.6088-2.67410.26411450.18472570X-RAY DIFFRACTION100
2.6741-2.74640.26881370.17632599X-RAY DIFFRACTION100
2.7464-2.82720.29151480.18642554X-RAY DIFFRACTION100
2.8272-2.91840.23661230.18452594X-RAY DIFFRACTION100
2.9184-3.02270.28921370.18212558X-RAY DIFFRACTION100
3.0227-3.14370.30031410.19582582X-RAY DIFFRACTION100
3.1437-3.28670.2941460.19612573X-RAY DIFFRACTION100
3.2867-3.45990.26771490.17142597X-RAY DIFFRACTION100
3.4599-3.67660.21891620.16322578X-RAY DIFFRACTION100
3.6766-3.96030.1981260.15552585X-RAY DIFFRACTION100
3.9603-4.35850.19211220.15052628X-RAY DIFFRACTION100
4.3585-4.98850.19271210.14072613X-RAY DIFFRACTION100
4.9885-6.2820.22281420.19592606X-RAY DIFFRACTION100
6.282-43.90540.2411350.21612640X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.1483 Å / Origin y: 16.6304 Å / Origin z: -3.235 Å
111213212223313233
T0.1117 Å20.016 Å2-0.0003 Å2-0.0293 Å2-0.0026 Å2--0.091 Å2
L0.8135 °2-0.1067 °2-0.0279 °2-1.3205 °2-0.0684 °2--0.5888 °2
S0.0925 Å °0.0219 Å °0.0164 Å °-0.0925 Å °-0.1108 Å °-0.0007 Å °0.0012 Å °0.0198 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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