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- PDB-2qgn: Crystal structure of tRNA isopentenylpyrophosphate transferase (B... -

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Basic information

Entry
Database: PDB / ID: 2qgn
TitleCrystal structure of 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
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 C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsForouhar, F. / Neely, H. / Abashidze, M. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Forouhar, F. / Neely, H. / Abashidze, M. / 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 tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans.
Authors: Forouhar, F. / Neely, H. / Abashidze, M. / 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. / Neely, H. / Abashidze, M. / 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
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4992
Polymers37,4031
Non-polymers961
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.855, 50.855, 204.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsPossibly dimer

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: miaA, BH2366 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9KAC3, EC: 2.5.1.8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 20 micro-g/ml Subtilisin, 5 mM DTT. Reservoir solution: 16% PEG 3350, 200 mM Ammonium tartrate, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→29.99 Å / Num. all: 21615 / Num. obs: 21615 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.082 / Net I/σ(I): 18.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.09 / Rsym value: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 136724.33 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THE FRIEDEL PAIRS WERE USED FOR PHASING. XtalView program has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1790 9.7 %RANDOM
Rwork0.225 ---
obs0.225 18491 80.9 %-
all-21615 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.3396 Å2 / ksol: 0.275607 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-8.72 Å28.97 Å20 Å2
2--8.72 Å20 Å2
3----17.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 5 35 1985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
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: 2.4→2.49 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 114 10.5 %
Rwork0.28 971 -
obs--47.7 %

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