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- PDB-7opk: Crystal structure of C. thermophilum Xrn2 -

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Basic information

Entry
Database: PDB / ID: 7opk
TitleCrystal structure of C. thermophilum Xrn2
Components5'-3' exoribonuclease
KeywordsRNA / degradation / metabolism / hydrolysis
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / DNA-templated transcription termination / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / nucleus
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain
Similarity search - Domain/homology
5'-3' exoribonuclease
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOverbeck, J.H. / Sprangers, R.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Observation of conformational changes that underlie the catalytic cycle of Xrn2.
Authors: Overbeck, J.H. / Stelzig, D. / Fuchs, A.L. / Wurm, J.P. / Sprangers, R.
History
DepositionJun 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-3' exoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2743
Polymers100,2251
Non-polymers492
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-19 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.780, 198.780, 69.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein 5'-3' exoribonuclease


Mass: 100225.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008830 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G0S058, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.94 Å3/Da / Density % sol: 68.76 % / Description: needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate, 20 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 31644 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 63.06 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.0679 / Rrim(I) all: 0.3085 / Net I/σ(I): 13.65
Reflection shellResolution: 3→3.107 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 1.89 / Num. unique obs: 3130 / CC1/2: 0.786 / CC star: 0.938 / Rpim(I) all: 0.4547 / Rrim(I) all: 2.037 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FQD

3fqd


Resolution: 3→49.69 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.8028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 1495 4.73 %
Rwork0.1802 30104 -
obs0.1822 31599 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.64 Å2
Refinement stepCycle: LAST / Resolution: 3→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 2 1 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345453
X-RAY DIFFRACTIONf_angle_d0.56337385
X-RAY DIFFRACTIONf_chiral_restr0.0429768
X-RAY DIFFRACTIONf_plane_restr0.0043966
X-RAY DIFFRACTIONf_dihedral_angle_d13.8622083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.34971460.27082689X-RAY DIFFRACTION99.93
3.1-3.210.3121450.25962678X-RAY DIFFRACTION99.75
3.21-3.340.30531360.24752724X-RAY DIFFRACTION99.69
3.34-3.490.26971460.22062693X-RAY DIFFRACTION99.86
3.49-3.670.24351370.18482732X-RAY DIFFRACTION99.97
3.67-3.90.20841150.17372763X-RAY DIFFRACTION99.97
3.9-4.20.2261340.16292699X-RAY DIFFRACTION99.93
4.2-4.620.19461600.14742738X-RAY DIFFRACTION100
4.63-5.290.16711240.15752756X-RAY DIFFRACTION99.97
5.29-6.660.21131260.172772X-RAY DIFFRACTION99.97
6.67-49.690.17891260.16382860X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 88.7994438754 Å / Origin y: -26.9454813922 Å / Origin z: 0.189443296424 Å
111213212223313233
T0.510833114257 Å2-0.0388777867492 Å20.0159460572308 Å2-0.369192229672 Å20.0169627824759 Å2--0.363787614915 Å2
L0.515851459601 °2-0.358614326645 °20.0638044963371 °2-1.42347337518 °20.121963263859 °2--1.31079752627 °2
S-0.0252331702967 Å °-0.0610257530379 Å °0.0669279316649 Å °-0.0522047573311 Å °0.0531987689013 Å °0.0376376977977 Å °-0.403091273499 Å °0.0117374259504 Å °-0.0300184688973 Å °
Refinement TLS groupSelection details: all

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