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- PDB-3ajv: Splicing endonuclease from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 3ajv
TitleSplicing endonuclease from Aeropyrum pernix
Components
  • Putative uncharacterized protein
  • tRNA-splicing endonuclease
KeywordsHYDROLASE / EndA / splicing endonuclease / tRNA splicing / Archaea Crenarchaea
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 / nucleic acid binding / lyase activity / membrane
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 / tRNA intron endonuclease catalytic domain-containing protein
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsYoshinari, S. / Watanabe, Y. / Okuda, M. / Shiba, T. / Inaoka, K.D. / Kurisu, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A Conserved Lysine Residue in the Crenarchaea-Specific Loop is Important for the Crenarchaeal Splicing Endonuclease Activity.
Authors: Okuda, M. / Shiba, T. / Inaoka, D.K. / Kita, K. / Kurisu, G. / Mineki, S. / Harada, S. / Watanabe, Y. / Yoshinari, S.
History
DepositionJun 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Other
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: tRNA-splicing endonuclease
C: Putative uncharacterized protein
D: tRNA-splicing endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,65616
Polymers82,6654
Non-polymers99212
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-65 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.334, 95.334, 253.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Putative uncharacterized protein / tRNA-splicing endonuclease subunit alpha


Mass: 20770.818 Da / Num. of mol.: 2 / Mutation: attached His-tag sequence at its N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE0685, APE1646, APE_0685 / Plasmid: pETDuet-6xHis-APE-EndA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q9YE85
#2: Protein tRNA-splicing endonuclease / tRNA-intron endonuclease


Mass: 20561.486 Da / Num. of mol.: 2 / Mutation: H133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: endA, APE_1646.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBF1, EC: 3.1.27.9
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20mM Tris-HCl (pH 8.0), 750mM KCl, 10% (v/v) glycerol, 0.2M NaCl, 0.1M phosphate-citrate (pH 4.2), 10% (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A11
SYNCHROTRONPhoton Factory BL-17A21.0717
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDDec 13, 2008
ADSC QUANTUM 2702CCDNov 28, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.07171
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.946
11K, H, -L20.054
ReflectionResolution: 1.7→50 Å / Num. all: 92608 / Num. obs: 90770 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.1 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.723 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22893 4695 5.1 %RANDOM
Rwork0.21751 ---
all0.21809 92608 --
obs0.21809 88149 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å20 Å20 Å2
2--4.14 Å20 Å2
3----8.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 62 549 5947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225736
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9867778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0921.142254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0715966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0711575
X-RAY DIFFRACTIONr_chiral_restr0.1050.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214402
X-RAY DIFFRACTIONr_mcbond_it0.9441.53521
X-RAY DIFFRACTIONr_mcangle_it1.58925671
X-RAY DIFFRACTIONr_scbond_it2.47532215
X-RAY DIFFRACTIONr_scangle_it3.9654.52092
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 290 -
Rwork0.306 5530 -
obs-5530 83.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.20270.06720.42590.3261-0.31541.6772-0.0198-0.08360.04280.0824-0.02160.0248-0.0884-0.13740.04130.08470.0417-0.01340.1365-0.03050.06324.75111.678251.293
20.7187-0.32650.24871.0142-0.10611.7764-0.00170.02140.045-0.1168-0.0095-0.0029-0.2676-0.02920.01110.0641-0.0036-0.0130.0289-0.00930.078415.19527.601213.435
30.8336-0.33770.26070.6642-0.19731.93680.06270.18750.0188-0.2228-0.1173-0.0153-0.02580.02560.05460.10110.01220.00510.0657-0.00360.034522.30713.983191.014
40.8036-0.3480.13511.1811-0.15592.2934-0.0627-0.0911-0.05140.11730.0714-0.03080.18620.2107-0.00860.0420.01660.00370.05330.00090.085631.855-0.492227.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 170
2X-RAY DIFFRACTION2B7 - 186
3X-RAY DIFFRACTION3C10 - 170
4X-RAY DIFFRACTION4D9 - 186

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