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- PDB-3exa: Crystal structure of the full-length tRNA isopentenylpyrophosphat... -

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Basic information

Entry
Database: PDB / ID: 3exa
TitleCrystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.
ComponentstRNA delta(2)-isopentenylpyrophosphate transferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ATP-binding / Nucleotide-binding / Nucleotidyltransferase / tRNA processing
Function / homology
Function and homology information


tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / tRNA processing / ATP binding
Similarity search - Function
Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain / IPP transferase / Dimethylallyltransferase / IPP transferase / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain / IPP transferase / Dimethylallyltransferase / IPP transferase / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Forouhar, F. / Abashidze, M. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / 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 full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.
Authors: Forouhar, F. / Abashidze, M. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. ...Authors: Forouhar, F. / Abashidze, M. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA delta(2)-isopentenylpyrophosphate transferase
B: tRNA delta(2)-isopentenylpyrophosphate transferase
C: tRNA delta(2)-isopentenylpyrophosphate transferase
D: tRNA delta(2)-isopentenylpyrophosphate transferase


Theoretical massNumber of molelcules
Total (without water)149,6114
Polymers149,6114
Non-polymers00
Water10,178565
1
A: tRNA delta(2)-isopentenylpyrophosphate transferase
B: tRNA delta(2)-isopentenylpyrophosphate transferase


Theoretical massNumber of molelcules
Total (without water)74,8062
Polymers74,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-14 kcal/mol
Surface area29450 Å2
MethodPISA
2
C: tRNA delta(2)-isopentenylpyrophosphate transferase
D: tRNA delta(2)-isopentenylpyrophosphate transferase


Theoretical massNumber of molelcules
Total (without water)74,8062
Polymers74,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-14 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.805, 73.824, 95.561
Angle α, β, γ (deg.)89.99, 93.73, 90.02
Int Tables number1
Space group name H-MP1
Detailspossibly monomer. However in both crystal and solution, the BH2366 molecules predominantly exist as dimers. At present, it is unknown what role an apo BH266 dimer plays.

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Components

#1: Protein
tRNA delta(2)-isopentenylpyrophosphate transferase / IPP transferase / Isopentenyl-diphosphate:tRNA isopentenyltransferase / IPTase / IPPT


Mass: 37402.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: locus_tag=BH2366 / Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2366, miaA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9KAC3, EC: 2.5.1.8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH (7.5), 100 mM NaCl, 5 mM DTT, and 0.025% (w/v) NaN3. Reservoir solution: 16% PEG 3350 and 200 mM Ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9788
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.3→29.9 Å / Num. all: 126922 / Num. obs: 89734 / % possible obs: 70.7 % / Observed criterion σ(F): 0.7 / Observed criterion σ(I): 0.7 / Redundancy: 1.5 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.038 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.083 / % possible all: 55.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBthen SOLVE/RESOLVEphasing
CNS1.2refinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 375722.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3936 4.6 %RANDOM
Rwork0.22 ---
obs0.22 85837 68.4 %-
all-125493 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9184 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--10.72 Å2-0.33 Å2-3.68 Å2
2--11.26 Å20.18 Å2
3----0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9684 0 0 565 10249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 286 4.5 %
Rwork0.249 6088 -
obs--50.7 %

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