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- PDB-1xdn: High resolution crystal structure of an editosome enzyme from try... -

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Basic information

Entry
Database: PDB / ID: 1xdn
TitleHigh resolution crystal structure of an editosome enzyme from trypanosoma brucei: RNA editing ligase 1
ComponentsRNA editing ligase MP52
KeywordsLIGASE / RNA editing / Trypanosoma brucei
Function / homology
Function and homology information


RNA ligase (ATP) / RNA ligase (ATP) activity / RNA modification / mitochondrial mRNA editing complex / kinetoplast / mRNA processing / mitochondrion / RNA binding / ATP binding / cytoplasm
Similarity search - Function
RNA ligase, Rnl2 / RNA ligase 1/2, C-terminal domain superfamily / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RNA-editing ligase 1, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsDeng, J. / Schnaufer, A. / Salavati, R. / Stuart, K.D. / Hol, W.G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1.
Authors: Deng, J. / Schnaufer, A. / Salavati, R. / Stuart, K.D. / Hol, W.G.
History
DepositionSep 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: RNA editing ligase MP52
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0693
Polymers31,5381
Non-polymers5312
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.911, 58.579, 52.984
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA editing ligase MP52


Mass: 31537.598 Da / Num. of mol.: 1 / Fragment: Adenylation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MP52 / Plasmid: pskB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD DE3 / References: GenBank: 11067037, UniProt: P86927*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, magnesium chloride, Tris, ATP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885, 0.97899, 0.96112
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.978991
30.961121
ReflectionResolution: 1.1→50 Å / Num. obs: 95711 / % possible obs: 86.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.293 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 33.8
Reflection shellHighest resolution: 1.1 Å / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 33.8 / Num. unique all: 95711 / Rsym value: 0.064 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.349 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14805 4149 5 %RANDOM
Rwork0.12822 ---
obs0.12923 78835 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.403 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.12 Å2
2---0.02 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 32 440 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212206
X-RAY DIFFRACTIONr_bond_other_d0.0020.021976
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9782993
X-RAY DIFFRACTIONr_angle_other_deg0.78434606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022428
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02457
X-RAY DIFFRACTIONr_nbd_refined0.220.2423
X-RAY DIFFRACTIONr_nbd_other0.250.22349
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.51319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91522128
X-RAY DIFFRACTIONr_scbond_it2.8293887
X-RAY DIFFRACTIONr_scangle_it4.2584.5865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.131 260
Rwork0.117 4798

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