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- PDB-3p1z: Crystal structure of the Aperopyrum pernix RNA splicing endonuclease -

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Basic information

Entry
Database: PDB / ID: 3p1z
TitleCrystal structure of the Aperopyrum pernix RNA splicing endonuclease
Components
  • Putative uncharacterized protein
  • tRNA-splicing endonuclease
KeywordsHYDROLASE / mixed antiparallel and parallel beta-sheet / heterotetramer / RNA splicing / RNA / Splicing endonuclease
Function / homology
Function and homology information


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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHirata, A.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA ...Title: Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop
Authors: Hirata, A. / Kitajima, T. / Hori, H.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: tRNA-splicing endonuclease
C: Putative uncharacterized protein
D: tRNA-splicing endonuclease
E: Putative uncharacterized protein
F: tRNA-splicing endonuclease
G: Putative uncharacterized protein
H: tRNA-splicing endonuclease
I: Putative uncharacterized protein
J: tRNA-splicing endonuclease
K: Putative uncharacterized protein
L: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)235,36812
Polymers235,36812
Non-polymers00
Water7,350408
1
A: Putative uncharacterized protein
B: tRNA-splicing endonuclease
C: Putative uncharacterized protein
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)78,4564
Polymers78,4564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-68 kcal/mol
Surface area29890 Å2
MethodPISA
2
E: Putative uncharacterized protein
F: tRNA-splicing endonuclease
G: Putative uncharacterized protein
H: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)78,4564
Polymers78,4564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-68 kcal/mol
Surface area29650 Å2
MethodPISA
3
I: Putative uncharacterized protein
J: tRNA-splicing endonuclease
K: Putative uncharacterized protein
L: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)78,4564
Polymers78,4564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-68 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.036, 135.036, 156.246
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative uncharacterized protein


Mass: 18599.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE0685 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q9YE85
#2: Protein
tRNA-splicing endonuclease / tRNA-intron endonuclease


Mass: 20628.555 Da / Num. of mol.: 6
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) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q9YBF1, EC: 3.1.27.9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.25M ammonium sulfate, 0.1M sodium citrate, 0.9M lithium sulfate, 1mM magnesium chloride, pH 5.6, 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: Feb 16, 2009
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 87511 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 64.04 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.84.50.778195
2.8-2.915.60.602199.1
2.91-3.0460.407199.8
3.04-3.26.20.246199.7
3.2-3.46.50.148199.8
3.4-3.666.80.098199.8
3.66-4.037.10.066199.9
4.03-4.627.70.0481100
4.62-5.818.20.0411100
5.81-508.10.033199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.239 Å / Occupancy max: 1 / Occupancy min: 0.63 / SU ML: 2.46 / σ(F): 0.06 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3182 3845 5.07 %
Rwork0.2602 --
obs0.2632 75772 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.576 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1692 Å2-0 Å2-0 Å2
2--7.1692 Å20 Å2
3----14.3385 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16173 0 0 408 16581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916507
X-RAY DIFFRACTIONf_angle_d1.28722278
X-RAY DIFFRACTIONf_dihedral_angle_d17.8796039
X-RAY DIFFRACTIONf_chiral_restr0.0772418
X-RAY DIFFRACTIONf_plane_restr0.0052901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83540.43111210.31622391X-RAY DIFFRACTION85
2.8354-2.87270.43371410.31872356X-RAY DIFFRACTION85
2.8727-2.91210.37831300.3072431X-RAY DIFFRACTION89
2.9121-2.95370.3841270.28982529X-RAY DIFFRACTION90
2.9537-2.99780.40661470.28652487X-RAY DIFFRACTION91
2.9978-3.04460.35791490.27042540X-RAY DIFFRACTION93
3.0446-3.09450.35991430.27492593X-RAY DIFFRACTION95
3.0945-3.14780.38451160.28732665X-RAY DIFFRACTION96
3.1478-3.2050.37891440.29772640X-RAY DIFFRACTION96
3.205-3.26670.37541350.27822667X-RAY DIFFRACTION97
3.2667-3.33330.3551590.26742740X-RAY DIFFRACTION98
3.3333-3.40580.34151350.27052683X-RAY DIFFRACTION98
3.4058-3.48490.36361520.28622748X-RAY DIFFRACTION99
3.4849-3.5720.331400.28222730X-RAY DIFFRACTION99
3.572-3.66860.35541550.26852711X-RAY DIFFRACTION99
3.6686-3.77640.30481430.26282729X-RAY DIFFRACTION99
3.7764-3.89830.30121430.24312778X-RAY DIFFRACTION100
3.8983-4.03750.29131450.25192724X-RAY DIFFRACTION100
4.0375-4.1990.31671640.25182782X-RAY DIFFRACTION100
4.199-4.38990.32251340.23652744X-RAY DIFFRACTION100
4.3899-4.6210.27121430.23822715X-RAY DIFFRACTION100
4.621-4.91010.27271340.23072765X-RAY DIFFRACTION100
4.9101-5.28850.25261490.23562787X-RAY DIFFRACTION100
5.2885-5.81940.3181500.24872732X-RAY DIFFRACTION100
5.8194-6.65840.32221560.26082773X-RAY DIFFRACTION100
6.6584-8.37740.31141510.24872732X-RAY DIFFRACTION100
8.3774-41.2430.24941390.23332755X-RAY DIFFRACTION100

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