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- PDB-3pie: Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant -

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Basic information

Entry
Database: PDB / ID: 3pie
TitleCrystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant
Components5'->3' EXORIBONUCLEASE (Xrn1)
KeywordsHYDROLASE / Beta berrel / Tudor domain / Chromo domain / mRNA turnover / rRNA processing / RNA binding / DNA binding
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / rRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2620 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1050 / paz domain - #40 / SH3 type barrels. - #750 / Ribosomal Protein S8; Chain: A, domain 1 - #250 / Rossmann fold - #12390 / Helix Hairpins - #950 / : / : / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2620 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1050 / paz domain - #40 / SH3 type barrels. - #750 / Ribosomal Protein S8; Chain: A, domain 1 - #250 / Rossmann fold - #12390 / Helix Hairpins - #950 / : / : / : / 5'-3' exoribonuclease 1 / Xrn1, D1 domain / Exoribonuclease Xrn1, D2/D3 domain / 5'-3' exoribonuclease 1, SH3-like domain / Xrn1 SH3-like domain / Exoribonuclease Xrn1 D1 domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / paz domain / SH3 type barrels. - #30 / Ribosomal Protein S8; Chain: A, domain 1 / Helix Hairpins / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / SH3 type barrels. / Alpha Horseshoe / Ribosomal protein L2, domain 2 / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-3' exoribonuclease 1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChang, J.H. / Xiang, S. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural and biochemical studies of the 5' -> 3' exoribonuclease Xrn1.
Authors: Chang, J.H. / Xiang, S. / Xiang, K. / Manley, J.L. / Tong, L.
History
DepositionNov 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 5'->3' EXORIBONUCLEASE (Xrn1)
B: 5'->3' EXORIBONUCLEASE (Xrn1)
C: 5'->3' EXORIBONUCLEASE (Xrn1)
D: 5'->3' EXORIBONUCLEASE (Xrn1)


Theoretical massNumber of molelcules
Total (without water)529,3794
Polymers529,3794
Non-polymers00
Water0
1
A: 5'->3' EXORIBONUCLEASE (Xrn1)


Theoretical massNumber of molelcules
Total (without water)132,3451
Polymers132,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5'->3' EXORIBONUCLEASE (Xrn1)


Theoretical massNumber of molelcules
Total (without water)132,3451
Polymers132,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5'->3' EXORIBONUCLEASE (Xrn1)


Theoretical massNumber of molelcules
Total (without water)132,3451
Polymers132,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 5'->3' EXORIBONUCLEASE (Xrn1)


Theoretical massNumber of molelcules
Total (without water)132,3451
Polymers132,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.720, 132.289, 143.890
Angle α, β, γ (deg.)110.07, 105.70, 103.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
5'->3' EXORIBONUCLEASE (Xrn1)


Mass: 132344.812 Da / Num. of mol.: 4 / Mutation: E178Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0F22385g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CJ09
Sequence detailsE178Q IS AN ACTIVE SITE MUTATION. AMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 1-1245 IN UNIPROT ...E178Q IS AN ACTIVE SITE MUTATION. AMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 1-1245 IN UNIPROT DATABASE ENTRY Q6CJ09, PLUS A C-TERMINAL EXPRESSION TAG (RESIDUES 1246-1253), WAS USED FOR CRYSTALLIZATION. MOST OF THE RESIDUES FROM RESIDUE 463 TO 503, AND FROM RESIDUE 984 TO 1082 WERE MISSING IN THE COORDINATES DUE TO LACK OF ELECTRON DENSITY. SEVERAL RESIDUES WITHIN THESE RANGES WERE MODELED AS POLY-ALA SEGMENTS, AND ARE REPRESENTED AS UNK RESIDUES 469-487 AND 1038-1052 OF CHAIN A, UNK RESIDUES 469-487 AND 1036-1052 OF CHAIN B, UNK RESIDUES 469-487 AND 1038-1054 OF CHAIN C, AND UNK RESIDUES 469-487 OF CHAIN D. THESE RESIDUE NUMBERS ARE ARBITRARILY ASSIGNED. IT IS EXPECTED THAT RESIDUES 469-487 BELONG TO THE 463-503 SEGMENT, AND RESIDUES 1036-1054 BELONG TO THE 984-1082 SEGMENT.

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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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 0.9M LiCl, 13.5% PEG 6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 161626 / Num. obs: 156952 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→3 Å / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.857 / SU B: 41.844 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30476 7790 5 %RANDOM
Rwork0.24125 ---
obs0.24441 146829 97.22 %-
all-151028 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.675 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å23.39 Å23.59 Å2
2--0.81 Å22.86 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34009 0 0 0 34009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02234786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.96346933
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08654151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224.1181673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.746156238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.74715199
X-RAY DIFFRACTIONr_chiral_restr0.1090.25121
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02126170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.520930
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.809233714
X-RAY DIFFRACTIONr_scbond_it2.412313856
X-RAY DIFFRACTIONr_scangle_it3.9064.513219
X-RAY DIFFRACTIONr_rigid_bond_restr1.333334637
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→3.055 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 1120 -
Rwork0.313 21210 -
obs--96.94 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
158.87792.510725.9652
216.602-22.343884.5279
399.016543.95330.3397
467.6334-48.59484.9786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 1240
2X-RAY DIFFRACTION2B3 - 1240
3X-RAY DIFFRACTION3C3 - 1240
4X-RAY DIFFRACTION4D3 - 1240

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