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- PDB-6n6a: Vibrio cholerae Oligoribonuclease bound to pGG -

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Basic information

Entry
Database: PDB / ID: 6n6a
TitleVibrio cholerae Oligoribonuclease bound to pGG
Components
  • OligoribonucleaseOligonucleotidase
  • RNA (5'-R(P*GP*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 / 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 (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6233
Polymers21,6002
Non-polymers231
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-23 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.864, 89.864, 59.622
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 (bacteria) / Gene: orn, VC0395_A2743, VC395_0384 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: A5F3M7, UniProt: Q9KV17*PLUS, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#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.: 304 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
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: Dec 13, 2017
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: 1.5→47.329 Å / Num. obs: 44737 / % possible obs: 100 % / Redundancy: 11.8 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.105 / Rsym value: 0.101 / Net I/av σ(I): 6.4 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.5-1.5810.51.1570.764400.3691.2161.15799.7
1.58-1.6812.10.777161140.2310.8110.777100
1.68-1.79120.5251.457730.1570.5480.525100
1.79-1.94120.3252.353580.0970.3390.325100
1.94-2.1212.40.1893.849640.0560.1970.189100
2.12-2.37120.1186.145140.0350.1230.118100
2.37-2.7412.40.0818.739930.0240.0850.081100
2.74-3.3511.90.05612.133900.0170.0580.056100
3.35-4.7411.80.0415.726660.0120.0420.04100
4.74-47.32911.40.03516.115250.0110.0370.03599.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IGI

2igi


Resolution: 1.5→32.586 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.46
RfactorNum. reflection% reflection
Rfree0.1602 2236 5 %
Rwork0.1467 --
obs0.1474 44692 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.28 Å2 / Biso mean: 21.7096 Å2 / Biso min: 10.51 Å2
Refinement stepCycle: final / Resolution: 1.5→32.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 47 1 307 1824
Biso mean--14.6 35.36 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53260.28721370.26772578271599
1.5326-1.56830.2291380.214626422780100
1.5683-1.60750.19981390.187826532792100
1.6075-1.65090.19061370.179226082745100
1.6509-1.69950.19451400.160926382778100
1.6995-1.75440.18011360.157626382774100
1.7544-1.81710.17611400.166326232763100
1.8171-1.88980.16361370.150426452782100
1.8898-1.97580.15081390.152626342773100
1.9758-2.080.17471390.137226622801100
2.08-2.21020.15111410.13726402781100
2.2102-2.38090.15221410.144726732814100
2.3809-2.62040.15811400.146226562796100
2.6204-2.99930.14491400.139926932833100
2.9993-3.77790.1471440.132826912835100
3.7779-32.59390.14641480.13232782293099
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)
14.9864-2.2256-2.4253.42381.73392.6273-0.06070.0768-0.0857-0.15620.0074-0.020.0599-0.0210.09530.1547-0.0034-0.00690.07480.00910.0795-44.73466.84671.237
21.7194-0.8837-1.49691.50330.77611.99370.03160.1409-0.0084-0.1798-0.0450.0373-0.0718-0.18540.01160.1549-0.0048-0.0060.10690.00420.1016-47.426414.0985-2.0042
31.3127-0.27620.19931.4768-0.591.0963-0.0299-0.0613-0.00440.0238-0.0653-0.2455-0.09660.10620.09760.1301-0.01320.01580.1044-0.00120.1367-35.06126.31496.6498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:24)A1 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:99)A25 - 99
3X-RAY DIFFRACTION3(chain A and resid 100:181)A100 - 181

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