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- PDB-2zyz: Pyrobaculum aerophilum splicing endonuclease -

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Basic information

Entry
Database: PDB / ID: 2zyz
TitlePyrobaculum aerophilum splicing endonuclease
Components
  • Putative uncharacterized protein PAE0789
  • tRNA-splicing endonuclease
KeywordsSPLICING / splicing endonuclease / Crenarchaea / heterotetramer / RNA processing / Endonuclease / Hydrolase / Nuclease / tRNA processing
Function / homology
Function and homology information


tRNA-type intron splice site recognition and cleavage / tRNA-intron lyase / tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation / nuclease activity / nucleic acid binding / lyase activity
Similarity search - Function
tRNA-splicing endonuclease, archaeal short subfamily / tRNA intron endonuclease, N-terminal domain / tRNA intron endonuclease, N-terminal domain superfamily / tRNA intron endonuclease, N-terminal / tRNA intron endonuclease, N-terminal domain / 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; Chain: A, domain 1 - #10 ...tRNA-splicing endonuclease, archaeal short subfamily / tRNA intron endonuclease, N-terminal domain / tRNA intron endonuclease, N-terminal domain superfamily / tRNA intron endonuclease, N-terminal / tRNA intron endonuclease, N-terminal domain / 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; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / MutS, DNA mismatch repair protein, domain I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-splicing endonuclease / Uncharacterized protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsYoshinari, S. / Inaoka, D.K. / Watanabe, Y. / Shiba, T. / Kurisu, G. / Harada, S.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease
Authors: Yoshinari, S. / Shiba, T. / Inaoka, D.K. / Itoh, T. / Kurisu, G. / Harada, S. / Kita, K. / Watanabe, Y.
History
DepositionJan 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 25, 2012Group: Source and taxonomy
Revision 1.3Mar 13, 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: Putative uncharacterized protein PAE0789
B: tRNA-splicing endonuclease
C: Putative uncharacterized protein PAE0789
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)68,2554
Polymers68,2554
Non-polymers00
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-62 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.762, 70.726, 131.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein PAE0789 / splicing endonuclease structural subunit


Mass: 13321.423 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE0789 / Plasmid: pETDuet-PAE-EndA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q8ZYG6
#2: Protein tRNA-splicing endonuclease / splicing endonuclease catalytic subunit / tRNA-intron endonuclease


Mass: 20806.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE2269 / Plasmid: pETDuet-PAE-EndA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q8ZVI1, EC: 3.1.27.9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.5M LiSO4, 15% PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 72101 / Num. obs: 69133 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Redundancy: 8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 4 / Num. unique all: 6611 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→33.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.429 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25157 3500 5.1 %RANDOM
Rwork0.20975 ---
all0.2119 69133 --
obs0.2119 65559 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.906 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 0 443 4922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224885
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9886612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6665625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19422.679224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45115948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881548
X-RAY DIFFRACTIONr_chiral_restr0.1270.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023650
X-RAY DIFFRACTIONr_nbd_refined0.2250.22350
X-RAY DIFFRACTIONr_nbtor_refined0.320.23349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.215
X-RAY DIFFRACTIONr_mcbond_it1.1471.52986
X-RAY DIFFRACTIONr_mcangle_it1.89124707
X-RAY DIFFRACTIONr_scbond_it2.52432153
X-RAY DIFFRACTIONr_scangle_it3.7534.51877
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 233 -
Rwork0.283 4656 -
obs-4656 93.05 %

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