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- PDB-4j37: Crystal structure of the catalytic domain of human Pus1 -

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Basic information

Entry
Database: PDB / ID: 4j37
TitleCrystal structure of the catalytic domain of human Pus1
ComponentstRNA pseudouridine synthase A, mitochondrial
KeywordsRNA BINDING PROTEIN / beta sheet / pseudouridine synthase / tRNA / pre-tRNA / steroid receptor RNA activator / U2 snRNA / Isomerase
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 / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA 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 / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA 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: 1.75 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
DepositionFeb 5, 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 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: tRNA pseudouridine synthase A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2405
Polymers37,9501
Non-polymers2904
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.950, 51.950, 445.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-664-

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: pET47modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3
References: UniProt: Q9Y606, tRNA pseudouridine38-40 synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 18% PEG8000, 0.1 M MES, 0.3 M AmSO4, pH 6.5, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 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: 1.75→50 Å / Num. obs: 37347 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 11.45 % / Biso Wilson estimate: 21.81 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.17
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.78 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 1.33 / % possible all: 89.8

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Processing

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

4its


Resolution: 1.75→44.76 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 2309 6.18 %
Rwork0.2 --
obs0.202 37344 98.4 %
all-37344 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 15 184 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122471
X-RAY DIFFRACTIONf_angle_d1.2313332
X-RAY DIFFRACTIONf_dihedral_angle_d14.029929
X-RAY DIFFRACTIONf_chiral_restr0.076359
X-RAY DIFFRACTIONf_plane_restr0.007428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78810.29171260.29141928X-RAY DIFFRACTION89
1.7881-1.82970.33411290.2821999X-RAY DIFFRACTION93
1.8297-1.87540.31381290.27442078X-RAY DIFFRACTION95
1.8754-1.92610.29461400.25892090X-RAY DIFFRACTION97
1.9261-1.98280.31391380.24852134X-RAY DIFFRACTION99
1.9828-2.04680.25771450.22252163X-RAY DIFFRACTION100
2.0468-2.120.24751420.20322159X-RAY DIFFRACTION100
2.12-2.20480.25581460.19232207X-RAY DIFFRACTION100
2.2048-2.30520.24441450.18782184X-RAY DIFFRACTION100
2.3052-2.42670.22811490.1882202X-RAY DIFFRACTION100
2.4267-2.57870.24871450.18952232X-RAY DIFFRACTION100
2.5787-2.77780.22911490.18372208X-RAY DIFFRACTION100
2.7778-3.05730.24351520.19292279X-RAY DIFFRACTION100
3.0573-3.49950.20171480.18982271X-RAY DIFFRACTION100
3.4995-4.40840.2211570.17082337X-RAY DIFFRACTION100
4.4084-44.7770.22581690.2032564X-RAY DIFFRACTION100

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