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- PDB-2nre: Crystal structure of pseudoudirinde synthase TruA in complex with... -

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Basic information

Entry
Database: PDB / ID: 2nre
TitleCrystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Components
  • leucyl tRNA
  • tRNA pseudouridine synthase A
KeywordsISOMERASE/RNA / pseudouridine synthase / anticodon stem loop / tRNA / multisite specificity / ISOMERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine38-40 synthase / tRNA pseudouridine(38-40) synthase activity / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA binding / protein homodimerization activity
Similarity search - Function
Pseudouridine synthase I, catalytic domain, C-terminal subdomain / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / tRNA pseudouridine synthase A
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsHur, S. / Stroud, R.M.
CitationJournal: Mol.Cell / Year: 2007
Title: How U38, 39, and 40 of Many tRNAs Become the Targets for Pseudouridylation by TruA.
Authors: Hur, S. / Stroud, R.M.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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
F: leucyl tRNA
A: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6144
Polymers58,5362
Non-polymers782
Water00
1
F: leucyl tRNA
A: tRNA pseudouridine synthase A
hetero molecules

F: leucyl tRNA
A: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2298
Polymers117,0734
Non-polymers1564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)80.355, 80.355, 205.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsA molecule of id A forms a dimer with its crystallographic symmetry mate (y,x,-z), and F is the substrate tRNA bound to the enzyme.

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Components

#1: RNA chain leucyl tRNA


Mass: 28094.645 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Occurs naturally in E. coli. Synthesized by T7 in vitro transcription
#2: Protein tRNA pseudouridine synthase A / tRNA-uridine isomerase I / tRNA pseudouridylate synthase I / PSU-I


Mass: 30441.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: truA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3
References: UniProt: P07649, tRNA pseudouridine38-40 synthase
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2K3 Citrate11
3spermine11
4H2O11
5PEG 335012
6K3 Citrate12
7spermine12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 9, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. all: 6998 / Num. obs: 6998 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.172 / Net I/σ(I): 9.53
Reflection shellResolution: 4→4.14 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.38 / Num. unique all: 664 / Rsym value: 0.531 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DJ0 and 1EHZ

1dj0

1ehz


Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.708 / SU B: 71.759 / SU ML: 0.98 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 1.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS parameter was refined for tRNA (treated as a single TLS group)
RfactorNum. reflection% reflectionSelection details
Rfree0.35735 328 5.3 %RANDOM
Rwork0.25946 ---
all0.26462 5809 --
obs0.26462 5809 89.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.36 Å20 Å2
2--0.71 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 1196 2 0 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3272.3814945
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6522.574101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.79815328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.921519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3080.31899
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.52221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.340.5162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.76221292
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37832081
X-RAY DIFFRACTIONr_scbond_it0.37422152
X-RAY DIFFRACTIONr_scangle_it0.63232864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 23 -
Rwork0.24 343 -
obs--75.15 %
Refinement TLS params.Method: refined / Origin x: -13.558 Å / Origin y: -28.623 Å / Origin z: 25.55 Å
111213212223313233
T0.8532 Å2-0.5022 Å20.0326 Å2-0.2332 Å20.0264 Å2--0.2665 Å2
L0.7861 °21.9651 °2-0.9894 °2-5.1351 °2-2.0272 °2--2.1378 °2
S-0.2476 Å °0.5527 Å °-0.2204 Å °-0.5464 Å °0.4767 Å °0.2514 Å °0.0983 Å °-0.1231 Å °-0.2291 Å °

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