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- PDB-6n6h: Vibrio cholerae Oligoribonuclease bound to pCpU -

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Basic information

Entry
Database: PDB / ID: 6n6h
TitleVibrio cholerae Oligoribonuclease bound to pCpU
Components
  • OligoribonucleaseOligonucleotidase
  • RNA (5'-R(P*CP*U)-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 / DNA metabolic process / 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 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.757 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
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5443
Polymers21,5212
Non-polymers231
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-27 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.070, 89.070, 60.143
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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: A0A0H6V4D7, UniProt: Q9KV17*PLUS, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*CP*U)-3')


Mass: 566.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 209 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
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: 1.757→47.43 Å / Num. all: 27804 / Num. obs: 27804 / % possible obs: 99.9 % / Redundancy: 12 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Rsym value: 0.059 / Net I/av σ(I): 7.4 / Net I/σ(I): 21.8 / Num. measured all: 334350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.76-1.8511.90.9860.840010.2971.030.98699.6
1.85-1.9611.90.5631.437870.170.5890.563100
1.96-2.1120.32.635860.090.3130.3100
2.1-2.2712.40.1694.633460.050.1760.169100
2.27-2.4812.10.116.930670.0330.1150.11100
2.48-2.7812.10.0759.627890.0220.0780.075100
2.78-3.2112.10.05112.324880.0150.0530.051100
3.21-3.9312.10.03814.621150.0110.040.038100
3.93-5.5511.90.03514.816610.010.0360.035100
5.55-47.4311.30.03513.69640.0110.0370.03599.9

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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: 1.757→35.791 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.1837 1390 5 %
Rwork0.1605 --
obs0.1617 27777 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.81 Å2 / Biso mean: 36.2918 Å2 / Biso min: 19.37 Å2
Refinement stepCycle: final / Resolution: 1.757→35.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 41 1 210 1721
Biso mean--48.05 47.31 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7565-1.81930.27491370.26952602273999
1.8193-1.89210.26341360.224326052741100
1.8921-1.97820.25521350.196926122747100
1.9782-2.08250.22361330.181826092742100
2.0825-2.2130.20221460.168126122758100
2.213-2.38380.18271310.169426392770100
2.3838-2.62360.18341450.172326412786100
2.6236-3.00310.19011370.165426332770100
3.0031-3.7830.17891440.149326662810100
3.783-35.79820.15431460.139527682914100
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)
15.5592-2.326-1.07244.16371.82963.741-0.01990.2854-0.4215-0.53230.0058-0.18420.09590.1829-0.0110.3516-0.03240.10480.1884-0.03260.2913-38.03384.2715-4.2819
23.1128-0.7323-1.711.95130.34592.3277-0.06350.2099-0.1841-0.224-0.01290.04230.0427-0.19340.07920.2372-0.0227-0.01270.1794-0.02060.1751-47.738310.5554-0.1792
32.3184-1.34251.26051.3966-1.79482.8046-0.1466-0.1170.08750.2218-0.1324-0.4147-0.38660.19530.25380.2595-0.05460.00240.22980.01780.3312-29.72618.17318.7625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:15)A1 - 15
2X-RAY DIFFRACTION2(chain A and resid 16:127)A16 - 127
3X-RAY DIFFRACTION3(chain A and resid 128:181)A128 - 181

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