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- PDB-4iqm: Crystal structure of the catalytic domain of human Pus1 -

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Basic information

Entry
Database: PDB / ID: 4iqm
TitleCrystal structure of the catalytic domain of human Pus1
ComponentstRNA pseudouridine synthase A, mitochondrial
KeywordsRNA BINDING PROTEIN / pseudouridine synthase / RNA modification / tRNA / pre-tRNA / steroid receptor RNA activator / U2 snRNA
Function / homology
Function and homology information


mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol ...mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / RNA splicing / mRNA processing / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Pseudouridine synthase PUS1/ PUS2-like / 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 ...Pseudouridine synthase PUS1/ PUS2-like / 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
Pseudouridylate synthase 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCzudnochowski, N. / Finer-Moore, J.S. / Stroud, R.M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different ...Title: In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities.
Authors: Czudnochowski, N. / Wang, A.L. / Finer-Moore, J. / Stroud, R.M.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Other
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.5Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: tRNA pseudouridine synthase A, mitochondrial


Theoretical massNumber of molelcules
Total (without water)37,9501
Polymers37,9501
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.570, 42.310, 71.810
Angle α, β, γ (deg.)90.00, 117.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-569-

HOH

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Components

#1: Protein tRNA pseudouridine synthase A, mitochondrial / tRNA pseudouridine(38-40) synthase / tRNA pseudouridylate synthase I / tRNA-uridine isomerase I


Mass: 37950.359 Da / Num. of mol.: 1 / Fragment: catalytic domain (unp residues 79-408)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUS1, PP8985 / Plasmid: pET47mod / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3
References: UniProt: Q9Y606, tRNA pseudouridine38-40 synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% w/v PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, 1 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2012 / Details: monochromator
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 29280 / Num. obs: 29280 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 18.98 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.8499 Å / Redundancy: 3 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.75 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
PHASERphasing
ELVESrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ITS

4its


Resolution: 1.8→19.733 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1464 5 %
Rwork0.1863 --
obs0.1883 29279 98.63 %
all-29279 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 0 149 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072579
X-RAY DIFFRACTIONf_angle_d1.053484
X-RAY DIFFRACTIONf_dihedral_angle_d13.703984
X-RAY DIFFRACTIONf_chiral_restr0.074378
X-RAY DIFFRACTIONf_plane_restr0.004449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.86430.33041450.26542768X-RAY DIFFRACTION99
1.8643-1.93890.27511470.232781X-RAY DIFFRACTION100
1.9389-2.02710.27291480.21872804X-RAY DIFFRACTION99
2.0271-2.13380.26511460.18762781X-RAY DIFFRACTION99
2.1338-2.26740.24121460.18712776X-RAY DIFFRACTION100
2.2674-2.44210.23521470.19182789X-RAY DIFFRACTION99
2.4421-2.68730.23451480.19222799X-RAY DIFFRACTION99
2.6873-3.07490.2311450.19272776X-RAY DIFFRACTION99
3.0749-3.86930.21831460.17382764X-RAY DIFFRACTION97
3.8693-19.73420.17491460.15792777X-RAY DIFFRACTION95

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