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- PDB-1a79: CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOC... -

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Basic information

Entry
Database: PDB / ID: 1a79
TitleCRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII
ComponentsTRNA ENDONUCLEASE
KeywordsENDONUCLEASE / TRNA ENDONUCLEASE
Function / homology
Function and homology information


tRNA-type intron splice site recognition and cleavage / tRNA-intron lyase / tRNA-intron endonuclease 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
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsLi, H. / Trotta, C.R. / Abelson, J.N.
CitationJournal: Science / Year: 1998
Title: Crystal structure and evolution of a transfer RNA splicing enzyme.
Authors: Li, H. / Trotta, C.R. / Abelson, J.
History
DepositionMar 23, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRNA ENDONUCLEASE
B: TRNA ENDONUCLEASE
C: TRNA ENDONUCLEASE
D: TRNA ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,96310
Polymers78,9834
Non-polymers9806
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-111 kcal/mol
Surface area29420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.950, 80.040, 193.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.958213, 0.27951, 0.060843), (0.265275, 0.947859, -0.176616), (-0.107037, -0.153096, -0.982397)92.7452, -7.6424, 79.7142
2given(-0.752995, -0.619023, 0.22318), (-0.617182, 0.546763, -0.565806), (0.228221, -0.563792, -0.79376)75.4063, 57.8017, 75.5218
3given(0.073066, -0.696801, 0.713533), (-0.776877, -0.488403, -0.397398), (0.625399, -0.525291, -0.577015)8.6011, 68.0995, 64.2857

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Components

#1: Protein
TRNA ENDONUCLEASE


Mass: 19745.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): BLR (DE3) / References: UniProt: Q58819
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion / PH range low: 6 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 M1reservoirKCl
220-80 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.02 / Wavelength: 1.02, 1.54
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 7, 1997
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.541
ReflectionResolution: 2.3→100 Å / Num. obs: 75778 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 10.3
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.167 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 165549
Reflection shell
*PLUS
% possible obs: 65.4 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.857refinement
HKLdata reduction
HKLdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.28→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 6326 9.7 %RANDOM
Rwork0.2 ---
obs0.2 65480 77.2 %-
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---1.75 Å20 Å2
3---2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.28→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 14 65 5663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.28→2.36 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 282 8.1 %
Rwork0.302 3180 -
obs--40.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPOLGY.ELEMENTS
X-RAY DIFFRACTION3TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION4PARAM.SO4TOP.SO4
Software
*PLUS
Name: X-PLOR / Version: 3.857 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59
LS refinement shell
*PLUS
Rfactor obs: 0.302

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