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- PDB-4fz2: Crystal structure of the fourth type of archaeal tRNA splicing en... -

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Basic information

Entry
Database: PDB / ID: 4fz2
TitleCrystal structure of the fourth type of archaeal tRNA splicing endonuclease from Candidatus Micrarchaeum acidiphilum ARMAN-2
ComponentstRNA intron endonuclease
KeywordsHYDROLASE / tRNA splicing endonuclease
Function / homology
Function and homology information


tRNA-intron lyase activity / tRNA splicing, via endonucleolytic cleavage and ligation / nucleic acid binding / cytoplasm
Similarity search - Function
tRNA intron endonuclease, N-terminal domain / tRNA intron endonuclease, N-terminal domain superfamily / tRNA-splicing endonuclease / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / tRNA endonuclease-like domain superfamily / MutS, DNA mismatch repair protein, domain I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA intron endonuclease
Similarity search - Component
Biological speciesCandidatus Micrarchaeum acidiphilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.252 Å
AuthorsHirata, A. / Fujishima, K. / Yamagami, R. / Kawamura, T. / Banfiled, J.F. / Kanai, A. / Hori, H.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity
Authors: Hirata, A. / Fujishima, K. / Yamagami, R. / Kawamura, T. / Banfield, J.F. / Kanai, A. / Hori, H.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA intron endonuclease
B: tRNA intron endonuclease


Theoretical massNumber of molelcules
Total (without water)91,7652
Polymers91,7652
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-28 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.021, 112.021, 81.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein tRNA intron endonuclease


Mass: 45882.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Micrarchaeum acidiphilum (archaea)
Strain: ARMAN-2 / Gene: UNLARM2_0797 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: C7DIA5, EC: 3.1.27.9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 3350, 0.2M tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 53752 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 39.01 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 39.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 49.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(autosol)model building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(autosol)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.252→37.405 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7794 / SU ML: 1.79 / σ(F): 0.1 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2523 5.07 %RANDOM
Rwork0.2175 ---
obs0.2195 49748 92.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.545 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 129.61 Å2 / Biso mean: 48.8894 Å2 / Biso min: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1-7.5473 Å2-0 Å2-0 Å2
2--7.5473 Å20 Å2
3----15.0946 Å2
Refinement stepCycle: LAST / Resolution: 2.252→37.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 0 152 6456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066442
X-RAY DIFFRACTIONf_angle_d0.9798676
X-RAY DIFFRACTIONf_dihedral_angle_d18.2662398
X-RAY DIFFRACTIONf_chiral_restr0.07936
X-RAY DIFFRACTIONf_plane_restr0.0031096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2524-2.29570.35281440.29552323246784
2.2957-2.34260.31071070.26152455256284
2.3426-2.39350.31281510.25652383253484
2.3935-2.44920.32161370.26472418255586
2.4492-2.51040.34921540.25832483263788
2.5104-2.57820.34841360.26462456259288
2.5782-2.65410.2811260.25172603272991
2.6541-2.73970.2951300.24212553268389
2.7397-2.83760.31251290.2472592272191
2.8376-2.95120.32221340.24572621275592
2.9512-3.08540.27921520.24892697284995
3.0854-3.2480.28821230.24282768289197
3.248-3.45140.28941610.23572829299099
3.4514-3.71770.2361460.20062813295999
3.7177-4.09140.22791470.19162801294899
4.0914-4.68240.19681410.16982829297099
4.6824-5.89560.19091640.18022804296899
5.8956-37.41010.23211410.18912797293898

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