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- PDB-2xri: Crystal structure of human ERI1 exoribonuclease 3 -

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Basic information

Entry
Database: PDB / ID: 2xri
TitleCrystal structure of human ERI1 exoribonuclease 3
ComponentsERI1 EXORIBONUCLEASE 3
KeywordsHYDROLASE / METAL BINDING
Function / homology
Function and homology information


exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding
Similarity search - Function
: / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ERI1 exoribonuclease 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWelin, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Welin, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
CitationJournal: To be Published
Title: Crystal Structure of Human Eri1 Exoribonuclease 3
Authors: Welin, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, ...Authors: Welin, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
History
DepositionSep 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Non-polymer description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ERI1 EXORIBONUCLEASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9013
Polymers25,7851
Non-polymers1162
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.720, 76.900, 86.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

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Components

#1: Protein ERI1 EXORIBONUCLEASE 3 / PRION PROTEIN-INTERACTING PROTEIN / PRION INTERACTOR 1


Mass: 25784.811 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE
References: UniProt: O43414, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5 20% PEG MONOMETHYL ETHER 2000 0.2M TRIMETHYLAMINE N-OXIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.15→43.5 Å / Num. obs: 12879 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.1
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0H

1w0h


Resolution: 2.15→43.49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.134 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21014 644 5 %RANDOM
Rwork0.17497 ---
obs0.17674 12235 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 7 104 1776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221716
X-RAY DIFFRACTIONr_bond_other_d0.0010.021180
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9622322
X-RAY DIFFRACTIONr_angle_other_deg0.85832890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27824.87278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined0.2040.2301
X-RAY DIFFRACTIONr_nbd_other0.1710.21147
X-RAY DIFFRACTIONr_nbtor_refined0.180.2806
X-RAY DIFFRACTIONr_nbtor_other0.0840.2819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7431.51340
X-RAY DIFFRACTIONr_mcbond_other0.1251.5410
X-RAY DIFFRACTIONr_mcangle_it0.85121671
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6093827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0474.5651
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 46 -
Rwork0.199 875 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.9803 Å / Origin y: 12.7294 Å / Origin z: -19.0152 Å
111213212223313233
T-0.0941 Å20.005 Å20.0056 Å2--0.0859 Å20.005 Å2---0.0636 Å2
L1.1828 °2-0.1519 °2-1.2247 °2-1.3032 °20.2991 °2--3.2473 °2
S-0.0732 Å °-0.0861 Å °-0.0818 Å °-0.04 Å °-0.0033 Å °-0.1825 Å °0.1775 Å °0.1615 Å °0.0765 Å °

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