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- PDB-4its: Crystal structure of the catalytic domain of human Pus1 with MES ... -

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Basic information

Entry
Database: PDB / ID: 4its
TitleCrystal structure of the catalytic domain of human Pus1 with MES in the active site
ComponentstRNA pseudouridine synthase A, mitochondrial
KeywordsRNA BINDING PROTEIN / beta sheet / isomerase / 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 / 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, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / 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, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / 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: 1.85 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 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references

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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)38,5306
Polymers37,9501
Non-polymers5795
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA pseudouridine synthase A, mitochondrial
hetero molecules

A: tRNA pseudouridine synthase A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,06012
Polymers75,9012
Non-polymers1,15910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2930 Å2
ΔGint-85 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.860, 51.860, 446.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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(DE3)
References: UniProt: Q9Y606, tRNA pseudouridine38-40 synthase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 18% (w/v) PEG8000, 0.1 M MES, 0.2 M AmSO4 , pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2012 / Details: monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→44.91 Å / Num. all: 32146 / Num. obs: 32146 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.69
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 3.38 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-IceGUI interface to EPICS controldata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.91 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2000 6.22 %
Rwork0.1818 --
obs0.1845 32145 99.5 %
all-32146 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 32 154 2551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142455
X-RAY DIFFRACTIONf_angle_d1.5393310
X-RAY DIFFRACTIONf_dihedral_angle_d14.3920
X-RAY DIFFRACTIONf_chiral_restr0.113355
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8492-1.89540.27161340.22242014X-RAY DIFFRACTION98
1.8954-1.94660.23281390.20332090X-RAY DIFFRACTION100
1.9466-2.00390.25291380.19082103X-RAY DIFFRACTION99
2.0039-2.06860.24141390.18232089X-RAY DIFFRACTION100
2.0686-2.14250.21181400.17552103X-RAY DIFFRACTION100
2.1425-2.22830.20531390.16322093X-RAY DIFFRACTION100
2.2283-2.32970.22511400.16862116X-RAY DIFFRACTION99
2.3297-2.45260.23981420.17232140X-RAY DIFFRACTION100
2.4526-2.60620.21681430.18432147X-RAY DIFFRACTION100
2.6062-2.80740.25761420.19662153X-RAY DIFFRACTION100
2.8074-3.08990.2311450.19242173X-RAY DIFFRACTION100
3.0899-3.53680.2051450.17332199X-RAY DIFFRACTION100
3.5368-4.45540.20361500.15842256X-RAY DIFFRACTION99
4.4554-44.92530.23881640.20162469X-RAY DIFFRACTION99
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)
11.33420.5725-0.99873.2844-0.29542.6254-0.259-0.009-0.2886-0.14640.08930.06580.7477-0.16650.08020.4436-0.02890.0330.13950.01850.2251-0.3318-7.2498.9714
22.9704-0.5991-1.29382.33790.10244.39860.1613-0.20380.2430.10330.1102-0.0284-0.593-0.025-0.14640.2853-0.02720.00450.0995-0.01040.1714-1.780816.223223.3172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 82:187)
2X-RAY DIFFRACTION2(chain A and resid 188:399)

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