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- PDB-2nr0: Crystal structure of pseudoudirinde synthase TruA in complex with... -

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Basic information

Entry
Database: PDB / ID: 2nr0
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 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, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / 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: 3.9 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: leucyl tRNA
F: leucyl tRNA
G: leucyl tRNA
H: leucyl tRNA
A: tRNA pseudouridine synthase A
B: tRNA pseudouridine synthase A
C: tRNA pseudouridine synthase A
D: tRNA pseudouridine synthase A


Theoretical massNumber of molelcules
Total (without water)234,1458
Polymers234,1458
Non-polymers00
Water00
1
E: leucyl tRNA
F: leucyl tRNA
A: tRNA pseudouridine synthase A
B: tRNA pseudouridine synthase A


Theoretical massNumber of molelcules
Total (without water)117,0734
Polymers117,0734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: leucyl tRNA
H: leucyl tRNA
C: tRNA pseudouridine synthase A
D: tRNA pseudouridine synthase A


Theoretical massNumber of molelcules
Total (without water)117,0734
Polymers117,0734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.033, 149.292, 291.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMolecules of id A & B form a dimeric TruA, and E and F are the substrate tRNAs bound to them.Molecules of id C & D form a dimeric TruA, and G and H are the substrate tRNAs bound to them.

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Components

#1: RNA chain
leucyl tRNA


Mass: 28094.645 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Occurs naturally in E. coli. tRNA is obtained by 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.: 4
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

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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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M K3 Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2K3 Citrate11
3H2O11
4PEG 335012
5K3 Citrate12
6H2O12

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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: Dec 12, 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: 3.9→50 Å / Num. all: 24919 / Num. obs: 24919 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.213 / Net I/σ(I): 4.86
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.56 / Num. unique all: 2453 / Rsym value: 0.619 / % possible all: 93

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DJ0 (apo TruA enzyme) and 1EHZ (phe tRNA)

1dj0

1ehz


Resolution: 3.9→50 Å / Isotropic thermal model: MAXIMUM LIKELIHOOD / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3503 1163 -RANDOM
Rwork0.2982 ---
all-23996 --
obs-23996 89.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--42.99 Å20 Å20 Å2
2--3.382 Å20 Å2
3---39.608 Å2
Refinement stepCycle: LAST / Resolution: 3.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8278 5991 0 0 14269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010398
X-RAY DIFFRACTIONc_angle_deg1.28717
LS refinement shellResolution: 3.9→3.96 Å
RfactorNum. reflection
Rfree0.2928 53
Rwork0.3288 -
obs-911

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