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- PDB-7t2s: Structure of E. coli upec-117 Cap18 3'-5' exonuclease -

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Basic information

Entry
Database: PDB / ID: 7t2s
TitleStructure of E. coli upec-117 Cap18 3'-5' exonuclease
Components3'-5' exonuclease
KeywordsDNA BINDING PROTEIN / CBASS
Function / homology
Function and homology information


DNA replication proofreading / 3'-5' exonuclease activity / nucleic acid binding / cytosol
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
ACETATE ION / Ribonuclease T
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsLiang, Q. / Richey, S.T. / Ye, Q. / Lau, R.K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI148814 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structure and activity of a bacterial defense-associated 3'-5' exonuclease.
Authors: Liang, Q. / Richey, S.T. / Ur, S.N. / Ye, Q. / Lau, R.K. / Corbett, K.D.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,2772
Polymers21,2181
Non-polymers591
Water2,072115
1
A: 3'-5' exonuclease
hetero molecules

A: 3'-5' exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5544
Polymers42,4362
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3580 Å2
ΔGint-17 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.992, 98.992, 97.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-371-

HOH

31A-398-

HOH

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Components

#1: Protein 3'-5' exonuclease / Ribonuclease T


Mass: 21218.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rnt_1, BvCmsH19A_00963, G5696_22140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A494K842
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20mM Tris-HCl pH 7.5, 0.2M Li Sulfate, 0.1M Na Acetate, 0.1M HEPES pH 7.5, and 17% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791, 0.9195
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.91951
ReflectionResolution: 1.82→97.37 Å / Num. obs: 25945 / % possible obs: 99.9 % / Redundancy: 19.3 % / Biso Wilson estimate: 28.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.02 / Rrim(I) all: 0.088 / Net I/σ(I): 27.5
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.039 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1491 / CC1/2: 0.868 / Rpim(I) all: 0.242 / Rrim(I) all: 1.062 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→85.73 Å / SU ML: 0.299 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 28.6075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1303 5.03 %
Rwork0.2222 24595 -
obs0.2236 25898 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.67 Å2
Refinement stepCycle: LAST / Resolution: 1.82→85.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 4 115 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121444
X-RAY DIFFRACTIONf_angle_d1.04081954
X-RAY DIFFRACTIONf_chiral_restr0.0616214
X-RAY DIFFRACTIONf_plane_restr0.009248
X-RAY DIFFRACTIONf_dihedral_angle_d12.6588516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.890.33621520.32472648X-RAY DIFFRACTION99.43
1.89-1.980.3551420.30842675X-RAY DIFFRACTION99.96
1.98-2.080.3731330.31822690X-RAY DIFFRACTION100
2.08-2.210.31141360.28212699X-RAY DIFFRACTION99.93
2.21-2.380.31381600.2732686X-RAY DIFFRACTION100
2.38-2.620.27841360.25372734X-RAY DIFFRACTION100
2.62-30.2691580.23362722X-RAY DIFFRACTION100
3-3.780.24991320.19562788X-RAY DIFFRACTION100
3.78-85.730.17921540.1712953X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.8980420785 Å / Origin y: 44.7304485157 Å / Origin z: 50.9489171232 Å
111213212223313233
T0.243063520512 Å20.00494881102579 Å20.0718940380636 Å2-0.386434419088 Å2-0.204167281818 Å2--0.357440143246 Å2
L1.97968473643 °20.703539058134 °20.438177702017 °2-2.53399741479 °20.447314529498 °2--2.02556619279 °2
S0.125714493516 Å °-0.510907284545 Å °0.366869633831 Å °0.31596318531 Å °-0.412994289515 Å °0.558168968024 Å °-0.136273276986 Å °-0.0750471893326 Å °0.146161570692 Å °
Refinement TLS groupSelection details: chain A

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