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- PDB-6n6g: Vibrio cholerae Oligoribonuclease bound to pCG -

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Basic information

Entry
Database: PDB / ID: 6n6g
TitleVibrio cholerae Oligoribonuclease bound to pCG
Components
  • OligoribonucleaseOligonucleotidase
  • RNA (5'-R(P*CP*G)-3')
Keywordsrna binding protein/rna / 3'-5' exoribonuclease / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / 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
RNA / Oligoribonuclease / Oligoribonuclease
Similarity search - Component
Biological speciesVibrio cholerae (unknown)
synthetic construct (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.018 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123609 United States
CitationJournal: Elife / Year: 2019
Title: A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.
Authors: Kim, S.K. / Lormand, J.D. / Weiss, C.A. / Eger, K.A. / Turdiev, H. / Turdiev, A. / Winkler, W.C. / Sondermann, H. / Lee, V.T.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligoribonuclease
D: RNA (5'-R(P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5833
Polymers21,5602
Non-polymers231
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-24 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.976, 88.976, 59.906
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Oligoribonuclease / Oligonucleotidase


Mass: 20954.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (unknown) / Gene: orn / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): BL21DE3
References: UniProt: A0A0H6V4D7, UniProt: Q9KV17*PLUS, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*CP*G)-3')


Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BisTris (pH 5.5), 17% polyethylene glycol 3350, and 20% xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.018→47.295 Å / Num. all: 18345 / Num. obs: 18345 / % possible obs: 99.9 % / Redundancy: 12 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.087 / Rsym value: 0.083 / Net I/av σ(I): 8.3 / Net I/σ(I): 20.6 / Num. measured all: 219716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.02-2.1311.61.1620.726210.3531.2161.16299.4
2.13-2.26120.6981.125030.210.730.698100
2.26-2.41120.4681.723650.140.4890.468100
2.41-2.612.40.3142.522070.0930.3270.314100
2.6-2.8512.10.1784.320260.0530.1850.178100
2.85-3.1912.20.0967.818390.0280.10.096100
3.19-3.68120.05213.516430.0160.0540.052100
3.68-4.51120.03618.313930.0110.0380.036100
4.51-6.3811.90.03220.111010.0090.0330.032100
6.38-47.295110.02721.36470.0080.0280.02799.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6A

6n6a


Resolution: 2.018→35.716 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.89
RfactorNum. reflection% reflection
Rfree0.1869 916 5 %
Rwork0.1615 --
obs0.1629 18322 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.3 Å2 / Biso mean: 43.8842 Å2 / Biso min: 23.84 Å2
Refinement stepCycle: final / Resolution: 2.018→35.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 44 1 158 1672
Biso mean--48.74 51.82 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0176-2.1240.28141160.23982446256299
2.124-2.2570.21361390.197624342573100
2.257-2.43130.23521220.191424762598100
2.4313-2.67590.22161320.188124712603100
2.6759-3.06290.20951390.174324882627100
3.0629-3.85820.17961310.146924972628100
3.8582-35.72190.14851370.139825942731100
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)
14.0037-0.8143-1.58962.60780.10742.659-0.08020.2795-0.1338-0.2761-0.0252-0.01010.0733-0.20230.11020.2857-0.0210.00310.1887-0.0110.1801-47.019213.1815-0.1554
22.4937-0.33950.5042.3382-1.20291.9573-0.1493-0.0413-0.2416-0.1075-0.0972-0.3782-0.03320.20640.25040.3112-0.02780.0720.26220.00320.338-35.88035.87654.4755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:88)A1 - 88
2X-RAY DIFFRACTION2(chain A and resid 89:181)A89 - 181

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