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- PDB-3p1y: Crystal structure of the chimeric Archaeoglobus fulgidus RNA spli... -

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Basic information

Entry
Database: PDB / ID: 3p1y
TitleCrystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity
ComponentstRNA-splicing endonuclease
KeywordsHYDROLASE / Protein homodimer / RNA splicing endonuclease / broad substrate specificity
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
Similarity search - Function
Trna Endonuclease; Chain: A, domain 1 - #150 / tRNA-splicing endonuclease, archaeal long subfamily / 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 Endonuclease; Chain: A, domain 1 - #150 / tRNA-splicing endonuclease, archaeal long subfamily / 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-splicing endonuclease
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Aeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 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-splicing endonuclease
B: tRNA-splicing endonuclease
C: tRNA-splicing endonuclease
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)148,3264
Polymers148,3264
Non-polymers00
Water5,441302
1
A: tRNA-splicing endonuclease
B: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)74,1632
Polymers74,1632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-16 kcal/mol
Surface area27250 Å2
MethodPISA
2
C: tRNA-splicing endonuclease
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)74,1632
Polymers74,1632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-16 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.770, 104.642, 165.303
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
tRNA-splicing endonuclease / tRNA-intron endonuclease


Mass: 37081.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Chimera protein of tRNA-splicing endonuclease from Archaeoglobus fulgidus (UNP residues 2-173), a insertion of UNP residues 39-53 of tRNA-splicing endonuclease from Aeropyrum pernix, tRNA- ...Details: Chimera protein of tRNA-splicing endonuclease from Archaeoglobus fulgidus (UNP residues 2-173), a insertion of UNP residues 39-53 of tRNA-splicing endonuclease from Aeropyrum pernix, tRNA-splicing endonuclease from Archaeoglobus fulgidus (UNP residues 179-188)
Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Aeropyrum pernix (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O29362, UniProt: Q9YBF1, EC: 3.1.27.9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.2M ammonium sulfate, 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate, 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: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 88892 / % possible obs: 99.7 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.05-2.1210.80.673197.1
2.12-2.2112.50.53199.8
2.21-2.31140.436199.9
2.31-2.4314.80.3481100
2.43-2.5815.10.2621100
2.58-2.7815.10.1821100
2.78-3.0615.10.1151100
3.06-3.51150.0761100
3.51-4.4214.10.0651100
4.42-5014.20.044199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→38.89 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2867 8397 9.4 %
Rwork0.2471 --
obs0.2498 84124 93.9 %
Solvent computationBsol: 49.8043 Å2
Displacement parametersBiso mean: 35.7352 Å2
Baniso -1Baniso -2Baniso -3
1-6.723 Å20 Å20 Å2
2--0.397 Å20 Å2
3----7.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10424 0 0 302 10726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4731.5
X-RAY DIFFRACTIONc_scbond_it2.3032
X-RAY DIFFRACTIONc_mcangle_it2.3382
X-RAY DIFFRACTIONc_scangle_it3.4482.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.05-2.120.36866680.3165X-RAY DIFFRACTION
2.12-2.210.32587670.2767X-RAY DIFFRACTION
2.21-2.310.31457930.2614X-RAY DIFFRACTION
2.31-2.430.31018400.255X-RAY DIFFRACTION
2.43-2.580.32528460.2569X-RAY DIFFRACTION
2.58-2.780.30718480.261X-RAY DIFFRACTION
2.78-3.060.30268960.2513X-RAY DIFFRACTION
3.06-3.510.28628650.2532X-RAY DIFFRACTION
3.51-4.420.26139050.2303X-RAY DIFFRACTION
4.42-500.26699690.2408X-RAY DIFFRACTION
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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