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- PDB-1szw: Crystal structure of E. coli tRNA pseudouridine synthase TruD -

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Basic information

Entry
Database: PDB / ID: 1szw
TitleCrystal structure of E. coli tRNA pseudouridine synthase TruD
ComponentstRNA pseudouridine synthase D
KeywordsLYASE / Pseudouridine synthase / novel fold / rna modification / trud / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


tRNA pseudouridine13 synthase / tRNA pseudouridine(13) synthase activity / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
Pseudouridine synthase / TruD, insertion domain / Pseudouridine synthase, TruD, insertion domain superfamily / : / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. ...Pseudouridine synthase / TruD, insertion domain / Pseudouridine synthase, TruD, insertion domain superfamily / : / TruD, catalytic domain / Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD / Pseudouridine synthase, TruD, catalytic domain / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsEricsson, U.B. / Nordlund, P. / Hallberg, B.M. / Structural Proteomics in Europe (SPINE)
CitationJournal: Febs Lett. / Year: 2004
Title: X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold
Authors: Ericsson, U.B. / Nordlund, P. / Hallberg, B.M.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 6, 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 / struct_conn / 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine synthase D
B: tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)85,9342
Polymers85,9342
Non-polymers00
Water8,557475
1
A: tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)42,9671
Polymers42,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA pseudouridine synthase D


Theoretical massNumber of molelcules
Total (without water)42,9671
Polymers42,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.180, 108.110, 112.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA pseudouridine synthase D / Pseudouridylate synthase / Uracil hydrolyase


Mass: 42966.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TRUD / Plasmid: PT73.3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57261, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000MME, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.93219 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2003
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93219 Å / Relative weight: 1
ReflectionResolution: 2→79.06 Å / Num. all: 52753 / Num. obs: 52753 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.072 / Net I/σ(I): 15.9
Reflection shellResolution: 2→2.1 Å / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.234 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.176 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23913 1678 3.2 %RANDOM
Rwork0.19246 ---
all0.19397 51156 --
obs0.19397 51075 99.84 %-
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: 15.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 0 475 5727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215352
X-RAY DIFFRACTIONr_bond_other_d0.0040.024928
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9397235
X-RAY DIFFRACTIONr_angle_other_deg0.912311394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125660
X-RAY DIFFRACTIONr_chiral_restr0.1060.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026015
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021140
X-RAY DIFFRACTIONr_nbd_refined0.2040.21023
X-RAY DIFFRACTIONr_nbd_other0.2490.25467
X-RAY DIFFRACTIONr_nbtor_other0.0880.23174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.218
X-RAY DIFFRACTIONr_mcbond_it0.8981.53284
X-RAY DIFFRACTIONr_mcangle_it1.46725232
X-RAY DIFFRACTIONr_scbond_it2.45732068
X-RAY DIFFRACTIONr_scangle_it3.7624.52003
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 117
Rwork0.212 3757
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)
113.6188-17.59410.98535.7739-15.18820.3196-0.3960.7154-0.31541.75140.23531.7134-0.1669-1.86570.16070.2949-0.0697-0.0550.25610.05020.276130.149945.7014-31.499
20.93430.5091-1.10611.0111-1.10924.8684-0.0452-0.0745-0.14630.03840.09320.09320.4287-0.4694-0.04790.1325-0.0074-0.02110.14490.02150.188231.485629.976-8.7849
37.31981.75572.54562.49382.29252.93740.0456-0.3854-0.0349-0.2338-0.01510.37730.206-0.5307-0.03050.1095-0.0187-0.05060.16650.0390.234520.787944.3257-24.6249
418.3794.2908-6.46184.5941-1.70375.8662-0.1287-0.1401-0.0091-0.0960.07810.48460.016-0.53050.05060.08820.0149-0.02470.04680.02160.133426.643849.3028-21.3109
52.32680.66110.91522.6710.8084.0339-0.0694-0.00070.2148-0.09320.0275-0.06-0.40610.18150.04190.2028-0.01440.01010.0010.00050.11538.118757.6573-17.2435
61.7258-1.171-0.97323.95790.67825.7552-0.05350.0724-0.27440.0437-0.03180.00420.53530.18180.08530.0950.01160.01180.00470.00670.113842.965332.3273-20.4132
759.526127.7573-20.238113.2791-5.08433.04760.2142-2.3392.2306-0.6458-0.79710.6601-2.0750.50750.58290.32890.07410.00530.28390.00740.267139.496570.4864-3.5329
81.5587-1.0357-1.24751.95592.47584.70620.1256-0.0820.1398-0.0049-0.13060.1492-0.1624-0.55530.0050.16890.00460.01350.15430.02310.233324.650371.420218.6847
96.87734.58262.356423.8821-6.19474.6202-0.12350.61051.0706-0.3603-0.01541.7013-0.865-0.58630.13890.39090.0405-0.04060.3115-0.00280.369937.55979.39862.8609
106.5584-4.62730.044723.84725.94784.7836-0.19150.03590.72190.43390.14280.2004-0.48330.19030.04880.1752-0.04330.01970.07890.00850.148443.412673.55975.7421
112.3896-0.14821.10133.8802-0.69674.61060.17060.3153-0.10.0855-0.0525-0.17230.19160.6269-0.11810.13240.0155-0.0140.1866-0.07360.122651.515762.893110.7059
124.33070.55762.392.24162.65317.29580.1118-0.3103-0.22220.0356-0.21280.44740.3515-0.8870.1010.1688-0.03910.01430.1023-0.01480.203326.045158.13798.5895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 523 - 27
2X-RAY DIFFRACTION2AA6 - 15928 - 181
3X-RAY DIFFRACTION3AA160 - 180182 - 202
4X-RAY DIFFRACTION4AA188 - 212210 - 234
5X-RAY DIFFRACTION5AA213 - 302235 - 324
6X-RAY DIFFRACTION6AA303 - 341325 - 363
7X-RAY DIFFRACTION7BB1 - 523 - 27
8X-RAY DIFFRACTION8BB6 - 15928 - 181
9X-RAY DIFFRACTION9BB160 - 178182 - 200
10X-RAY DIFFRACTION10BB189 - 212211 - 234
11X-RAY DIFFRACTION11BB213 - 302235 - 324
12X-RAY DIFFRACTION12BB303 - 340325 - 362

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