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

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Basic information

Entry
Database: PDB / ID: 2nqp
TitleCrystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Components
  • tRNA pseudouridine synthase A
  • transfer RNA
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: 3.5 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
DepositionOct 31, 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: transfer RNA
A: tRNA pseudouridine synthase A
B: tRNA pseudouridine synthase A
C: tRNA pseudouridine synthase A
D: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,07711
Polymers149,8425
Non-polymers2356
Water0
1
F: transfer RNA
C: tRNA pseudouridine synthase A
D: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1949
Polymers88,9593
Non-polymers2356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA pseudouridine synthase A
B: tRNA pseudouridine synthase A


Theoretical massNumber of molelcules
Total (without water)60,8832
Polymers60,8832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.278, 128.585, 159.256
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 biological assembly unit of dimeric TruA. Molecules of id C, D and F form a biological assembly unit (C and D form a dimeric TruA enzyme and F is the substrate tRNA bound to the enzyme).

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Components

#1: RNA chain transfer RNA /


Mass: 28075.693 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Occurs naturally in E. coli. tRNA is obtained by in vitro transcription.
References: GenBank: 174437
#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
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
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: Jan 23, 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: 3.5→50 Å / Num. all: 25523 / Num. obs: 25523 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.236 / Net I/σ(I): 6.99
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.42 / Rsym value: 0.722 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.837 / Cor.coef. Fo:Fc free: 0.797 / SU B: 31.577 / SU ML: 0.501 / Cross valid method: THROUGHOUT / ESU R Free: 0.694 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27912 2384 10 %RANDOM
Rwork0.24601 ---
obs0.24936 21541 94.09 %-
all-21541 --
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: 37.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.34 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8318 1441 6 0 9765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02110103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2412.11814080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.04651050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6822.592409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3991578
X-RAY DIFFRACTIONr_chiral_restr0.0740.21602
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2770.25149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3350.26923
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2361
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.55265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42828473
X-RAY DIFFRACTIONr_scbond_it1.65334838
X-RAY DIFFRACTIONr_scangle_it2.6974.55607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 178 -
Rwork0.293 1404 -
obs--86.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.40254.3001-4.39921.9666-2.01192.05832.3087-3.47012.4214-1.3341-1.0997-0.0339-0.21122.6433-1.209-0.6842-0.2431-0.05110.8427-0.72941.1413-1.7309-40.864416.8144
25.50715.12652.16045.99123.68373.14270.54710.08670.8314-0.03180.3566-0.15570.0705-0.0678-0.9037-0.0978-0.03460.0316-0.1194-0.05550.0454-22.4499-38.738419.6135
39.45850.79762.99230.61790.38450.97840.2521-0.26960.12780.2560.0903-0.20910.3509-0.5243-0.3423-0.3149-0.10550.09280.0047-0.06190.1563-35.8109-25.649426.8037
417.380516.2064-8.68915.1117-8.10214.34390.18153.220.5861-0.60990.48684.709-2.8809-1.6243-0.66821.31920.53030.14610.47240.17140.5749-23.6234-26.32295.4124
58.80172.5832-3.47266.66736.186210.1560.03680.53580.43610.02430.8224-0.32170.53890.741-0.8592-0.2495-0.0164-0.0659-0.0624-0.16170.0471-11.8783-43.84192.7412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1FA3 - 73 - 7
2X-RAY DIFFRACTION1FA66 - 7077 - 81
3X-RAY DIFFRACTION2FA8 - 158 - 15
4X-RAY DIFFRACTION2FA20 - 2520 - 26
5X-RAY DIFFRACTION3FA26 - 4727 - 58
6X-RAY DIFFRACTION5FA48 - 6559 - 76
7X-RAY DIFFRACTION5FA16 - 2016 - 20

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