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- PDB-7n8w: Crystal structure of ERI2 nuclease bound to rAMP -

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Basic information

Entry
Database: PDB / ID: 7n8w
TitleCrystal structure of ERI2 nuclease bound to rAMP
ComponentsERI1 exoribonuclease 2
KeywordsHYDROLASE / HYDROLASE 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 / nucleic acid binding / zinc ion binding
Similarity search - Function
Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / ERI1 exoribonuclease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsThapar, R. / Arvai, A.S. / Tainer, J.A.
Funding support United States, 5items
OrganizationGrant numberCountry
Robert A. Welch Foundation
National Institutes of Health/National Cancer Institute (NIH/NCI)CA220430 United States
Other privateGAP Award (to R.T., J.A.T) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076660-04S1 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: To Be Published
Title: Crystal structure of ERI2 nuclease bound to rAMP
Authors: Thapar, R. / Arvai, A.S. / Tainer, J.A.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: ERI1 exoribonuclease 2
B: ERI1 exoribonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7529
Polymers59,9032
Non-polymers8487
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-86 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.832, 56.338, 75.852
Angle α, β, γ (deg.)90.000, 104.572, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 30 and (name N or name...
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA1 - 213
d_21ens_1SERLEUD1 - 213

NCS oper: (Code: givenMatrix: (-0.936361118806, 0.193294095175, -0.293027725581), (-0.0353982591461, -0.882482784683, -0.469010765321), (-0.34924893477, -0.428790773581, 0.833164842065)Vector: -51. ...NCS oper: (Code: given
Matrix: (-0.936361118806, 0.193294095175, -0.293027725581), (-0.0353982591461, -0.882482784683, -0.469010765321), (-0.34924893477, -0.428790773581, 0.833164842065)
Vector: -51.5081073618, -17.3704501062, -10.673173577)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ERI1 exoribonuclease 2 / Exonuclease domain-containing protein 1


Mass: 29951.580 Da / Num. of mol.: 2 / Fragment: exonuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERI2, EXOD1, KIAA1504 / Production host: Escherichia coli (E. coli)
References: UniProt: A8K979, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 14 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 9% MPEG 2K, 1% saturated Magnesium Sulfate, 5% Ethylene glycol, 200 mM Imidazole Malate buffer pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19057 / % possible obs: 90.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.79 Å2
Details: The number provided for unique reflections observed in data collection is that found after merging Friedel pairs. The number recorded for refinement counts the individual Friedel mates separately
Rrim(I) all: 0.104 / Net I/σ(I): 27.9
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 1820 / Rrim(I) all: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4l83

4l83


Resolution: 2.35→44.69 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 1529 4.9 %
Rwork0.179 29676 -
obs0.1812 31205 76.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.72 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 48 7 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223551
X-RAY DIFFRACTIONf_angle_d0.53944802
X-RAY DIFFRACTIONf_chiral_restr0.0408525
X-RAY DIFFRACTIONf_plane_restr0.0036599
X-RAY DIFFRACTIONf_dihedral_angle_d14.09291302
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.86165181966 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.4441620.33591261X-RAY DIFFRACTION35.91
2.43-2.510.3479850.33081628X-RAY DIFFRACTION46.69
2.51-2.610.31091030.31841959X-RAY DIFFRACTION55.97
2.61-2.730.3751180.29212177X-RAY DIFFRACTION62.64
2.73-2.880.31111240.29822678X-RAY DIFFRACTION76.1
2.88-3.060.34821580.28333070X-RAY DIFFRACTION86.4
3.06-3.290.29841670.24813252X-RAY DIFFRACTION93.01
3.29-3.620.31051750.20563358X-RAY DIFFRACTION95.93
3.62-4.150.24041760.16093410X-RAY DIFFRACTION97.79
4.15-5.220.13581830.12933455X-RAY DIFFRACTION98.43
5.23-44.690.17111780.12773428X-RAY DIFFRACTION97.83

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