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- PDB-2gjw: RNA Recognition and Cleavage by an Splicing Endonuclease -

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Basic information

Entry
Database: PDB / ID: 2gjw
TitleRNA Recognition and Cleavage by an Splicing Endonuclease
Components
  • 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
  • 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
  • 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
  • tRNA-splicing endonuclease
KeywordsHydrolase/RNA / Bulge-Helix-Bulge RNA-protein complex / Splicing Endonuclease Af / Hydrolase-RNA COMPLEX
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
Similarity search - Function
Trna Endonuclease; Chain: A, domain 1 - #150 / tRNA-splicing endonuclease, archaeal long 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 - #150 / tRNA-splicing endonuclease, archaeal long 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
RNA / RNA (> 10) / tRNA-splicing endonuclease
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXue, S. / Calvin, K. / Li, H.
CitationJournal: Science / Year: 2006
Title: RNA Recognition and Cleavage by an Splicing Endonuclease
Authors: Xue, S. / Calvin, K. / Li, H.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHOR STATES THAT THIS IS A HOMOLOGOUS MUTATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
F: 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
H: 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
I: 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
J: 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
L: 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
A: tRNA-splicing endonuclease
B: tRNA-splicing endonuclease
C: tRNA-splicing endonuclease
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)172,84010
Polymers172,84010
Non-polymers00
Water0
1
E: 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
F: 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
H: 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
A: tRNA-splicing endonuclease
B: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)86,4205
Polymers86,4205
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
J: 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
L: 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
C: tRNA-splicing endonuclease
D: tRNA-splicing endonuclease


Theoretical massNumber of molelcules
Total (without water)86,4205
Polymers86,4205
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.965, 140.413, 82.048
Angle α, β, γ (deg.)90.00, 111.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13E
23I
14F
24J
15H
25L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVALAG5 - 30810 - 313
21ILEILEVALVALDJ5 - 30810 - 313
12GLYGLYVALVALBH6 - 30712 - 313
22GLYGLYVALVALCI6 - 30712 - 313
13GGCCEA3 - 201 - 18
23GGCCID3 - 201 - 18
14UUA23A23FB3 - 141 - 12
24UUA23A23JE3 - 141 - 12
15AAGGHC15 - 201 - 6
25AAGGLF15 - 201 - 6

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: RNA chain 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'


Mass: 6059.706 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'


Mass: 3913.325 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'


Mass: 2236.395 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Protein
tRNA-splicing endonuclease / tRNA-intron endonuclease


Mass: 37105.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: endA / Plasmid: pET13b / Production host: Escherichia coli (E. coli) / References: UniProt: O29362, EC: 3.1.27.9

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION, HANGING DROP, PH 6.5, 303K, 0.12M AMMONIUM ACETATE, 35mM MAGNESIUM ACETATE, 50mM SODIUM CACODYLATE,10% ISOPROPANOL
Components of the solutions
IDNameCrystal-IDSol-ID
1AMMONIUM ACETATE11
2MAGNESIUM ACETATE11
3SODIUM CACODYLATE11
4ISOPROPANOL11
5H2O11
6AMMONIUM ACETATE12
7MAGNESIUM ACETATE12
8SODIUM CACODYLATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→35.09 Å / Num. all: 45000 / Num. obs: 40048 / % possible obs: 90.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Rsym value: 0.11
Reflection shellResolution: 2.85→2.92 Å / Rsym value: 0.608 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→35.09 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.807 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29646 1689 5 %RANDOM
Rwork0.24736 ---
obs0.24986 32074 83.94 %-
all-40048 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.72 Å2
2--2.49 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10186 1592 0 0 11778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8312.14816684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3551219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96922.904551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.939151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.58815116
X-RAY DIFFRACTIONr_chiral_restr0.1130.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.25772
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.28142
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3361.56067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.46529788
X-RAY DIFFRACTIONr_scbond_it3.09436079
X-RAY DIFFRACTIONr_scangle_it4.984.56888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A25290.05
2B25170.05
3E3790.04
4F2580.24
5H1280.19
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 144 -
Rwork0.312 2361 -
obs--77.2 %

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