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- PDB-1sgv: STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB) -

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Basic information

Entry
Database: PDB / ID: 1sgv
TitleSTRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)
ComponentstRNA pseudouridine synthase B
KeywordsLYASE / Hinged motion / tRNA modification / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


tRNA pseudouridine synthase activity / tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / peptidoglycan-based cell wall / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB, subfamily 2, C-terminal / tRNA Pseudouridine synthase II, C terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / PUA domain ...tRNA pseudouridine synthase II, TruB, subfamily 2, C-terminal / tRNA Pseudouridine synthase II, C terminal / tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Pseudouridine synthase, catalytic domain superfamily / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase B / tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaudhuri, B.N. / Chan, S. / Perry, L.J. / Yeates, T.O. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.
Authors: Chaudhuri, B.N. / Chan, S. / Perry, L.J. / Yeates, T.O.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2004ID: 1S71
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 B
B: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)67,7222
Polymers67,7222
Non-polymers00
Water8,125451
1
A: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)33,8611
Polymers33,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA pseudouridine synthase B


Theoretical massNumber of molelcules
Total (without water)33,8611
Polymers33,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.948, 94.100, 78.508
Angle α, β, γ (deg.)90.00, 100.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase


Mass: 33860.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: TRUB, RV2793C, MT2862.1, MTV002.58C, MB2816C / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-GOLD
References: UniProt: P62190, UniProt: P9WHP7*PLUS, pseudouridylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 298 K / Method: microseeding / pH: 7.5
Details: AMMONIUM SULFATE, TRIS BUFFER, PEG3350, pH 7.5, temperature 298K, microseeding
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH8.
20.3 M1dropNaCl
320 mg/mlprotein1drop
40.2 Mammonium sulfate1reservoir
50.1 MTris1reservoirpH8.5
625 %(w/v)PEG33501reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0322 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 1.9→40.2 Å / Num. obs: 51411 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % possible obs: 99.5 % / Redundancy: 3.6 % / Num. measured all: 184403
Reflection shell
*PLUS
% possible obs: 99.5 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K8W protein component

1k8w


Resolution: 1.9→40.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.491 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23947 2551 5 %RANDOM
Rwork0.20082 ---
obs0.20268 48859 99.43 %-
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: 20.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.35 Å2
2---0.43 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 0 451 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9775359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615524
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_restr0.0650.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21772
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3871.52607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74924150
X-RAY DIFFRACTIONr_scbond_it1.25431356
X-RAY DIFFRACTIONr_scangle_it2.2584.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 182
Rwork0.28 3521
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)
12.6396-0.4657-2.31483.54391.88373.58840.23610.11230.322-0.75560.2168-0.5189-0.58070.0578-0.45280.256-0.03410.07230.1656-0.00860.160815.349-1.20525.371
23.9918-1.5462-1.8913.05371.11112.58420.07940.10920.0865-0.14180.01990.0934-0.05050.0046-0.09940.02380.013-0.04370.15830.020.1207-6.7583.98343.054
32.54810.52481.29547.89341.15995.40840.01350.43110.0949-1.25-0.0749-0.4293-0.0680.26170.06140.425-0.00390.10460.2329-0.01630.102915.546-21.79711.223
41.8267-0.29360.58493.519-0.78642.5150.0351-0.0604-0.16790.22160.09390.23550.0831-0.1744-0.1290.03510.0082-0.02560.1870.03460.0783-25.841.43255.738
53.3709-2.16323.41593.0932-3.52657.69190.02570.19110.03490.1507-0.0076-0.06830.0570.1773-0.01810.39570.0066-0.0510.24580.03490.0414-12.141-1.68681.034
63.3805-0.4302-1.06149.58490.46944.12230.06250.2676-0.1083-0.6904-0.0115-0.0416-0.1021-0.0294-0.0510.13420.0382-0.02530.14630.02310.0507-22.97622.36342.285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 713 - 71
2X-RAY DIFFRACTION1AA200 - 226200 - 226
3X-RAY DIFFRACTION2AA72 - 19972 - 199
4X-RAY DIFFRACTION3AA227 - 292227 - 292
5X-RAY DIFFRACTION4BB1 - 711 - 71
6X-RAY DIFFRACTION4BB200 - 226200 - 226
7X-RAY DIFFRACTION5BB72 - 19972 - 199
8X-RAY DIFFRACTION6BB227 - 294227 - 294
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40.2 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.97
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.5
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / Rfactor Rfree: 0.33

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