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- PDB-7th0: Escherichia coli RpnA-S -

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Basic information

Entry
Database: PDB / ID: 7th0
TitleEscherichia coli RpnA-S
ComponentsRecombination-promoting nuclease RpnA
KeywordsANTITOXIN / toxin-antitoxin phage defense endonuclease abortive infection
Function / homologyTransposase (putative), YhgA-like / Recombination-promoting nuclease RpnA / Putative transposase, YhgA-like / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / double-stranded DNA endonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA recombination / Recombination-promoting nuclease RpnA
Function and homology information
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsZhong, A. / Hickman, A.B. / Storz, G. / Dyda, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins.
Authors: Zhong, A. / Jiang, X. / Hickman, A.B. / Klier, K. / Teodoro, G.I.C. / Dyda, F. / Laub, M.T. / Storz, G.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Recombination-promoting nuclease RpnA


Theoretical massNumber of molelcules
Total (without water)5,5181
Polymers5,5181
Non-polymers00
Water1448
1
A: Recombination-promoting nuclease RpnA

A: Recombination-promoting nuclease RpnA


Theoretical massNumber of molelcules
Total (without water)11,0362
Polymers11,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.020, 58.270, 38.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide Recombination-promoting nuclease RpnA


Mass: 5517.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain: K-12 / Gene: rpnA, yhgA, b3411, JW3374 / Production host: Escherichia coli (E. coli)
References: UniProt: P31667, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.5M LiCl 0.1M Tris HCl 30% PEG 6K 5 mM Fe(III)Cl / PH range: 8.3-9.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.36 Å / Num. obs: 3582 / % possible obs: 99.8 % / Redundancy: 13.48 % / CC1/2: 1 / Net I/σ(I): 43.46
Reflection shellResolution: 1.91→1.95 Å / Num. unique obs: 262 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.36 Å / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 108 3.02 %
Rwork0.225 3465 -
obs0.2258 3573 99.67 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.81 Å2 / Biso mean: 55.0758 Å2 / Biso min: 27.89 Å2
Refinement stepCycle: final / Resolution: 1.9→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms353 0 0 8 361
Biso mean---56.12 -
Num. residues----46
LS refinement shellResolution: 1.9→19.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.247 108 -
Rwork0.225 3465 -
all-3573 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.94040.77321.18095.3501-2.85034.44570.075-0.18810.14390.6074-0.18180.68170.0185-0.3370.45850.3153-0.010.02640.3907-0.0180.411915.246733.87489.7278
25.96783.061.82493.15682.1091.41940.8535-1.629-1.42480.4262-0.44960.38891.9266-1.04680.23420.6222-0.2883-0.10210.27830.12510.510413.203518.299712.1006
35.19041.2454-0.68326.53320.94314.07650.6007-1.92580.67631.0966-0.31033.51750.3064-1.2312-0.16230.6392-0.07940.21390.5113-0.04571.11145.58526.080111.7981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 244 through 268 )A244 - 268
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 280 )A269 - 280
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 289 )A281 - 289

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