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- PDB-6n6e: Vibrio cholerae Oligoribonuclease bound to pGA -

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Basic information

Entry
Database: PDB / ID: 6n6e
TitleVibrio cholerae Oligoribonuclease bound to pGA
Components
  • RNA (5'-R(P*GP*A)-3')
  • RNA exonuclease 2 homolog,Small fragment nuclease
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 / nucleic acid binding / Hydrolases; Acting on ester bonds / 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: 1.578 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: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6073
Polymers21,5842
Non-polymers231
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-22 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.615, 89.615, 59.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

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Components

#1: Protein RNA exonuclease 2 homolog,Small fragment nuclease


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*GP*A)-3')


Mass: 629.454 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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
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: Feb 11, 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: 1.578→47.311 Å / Num. all: 38266 / Num. obs: 38266 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 22.94 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.064 / Rsym value: 0.06 / Net I/av σ(I): 7.4 / Net I/σ(I): 17.8 / Num. measured all: 319761
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.58-1.668.30.9380.854730.3410.93898.7
1.66-1.768.40.6021.352510.2170.6410.602100
1.76-1.898.40.3592.149450.130.3830.359100
1.89-2.048.30.2113.645910.0770.2250.211100
2.04-2.238.30.1156.642390.0420.1220.115100
2.23-2.58.40.0769.738700.0270.0810.076100
2.5-2.888.60.05212.933990.0190.0550.052100
2.88-3.538.40.03814.329000.0140.0410.038100
3.53-4.998.30.03516.222870.0130.0370.03599.9
4.99-47.3117.80.03614.113110.0140.0390.03699.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6A

6n6a


Resolution: 1.578→47.311 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.45
RfactorNum. reflection% reflection
Rfree0.1588 1916 5.01 %
Rwork0.152 --
obs0.1524 38236 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.72 Å2 / Biso mean: 29.4033 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: final / Resolution: 1.578→47.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 46 1 266 1782
Biso mean--20.33 42.29 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061595
X-RAY DIFFRACTIONf_angle_d0.8082175
X-RAY DIFFRACTIONf_chiral_restr0.055242
X-RAY DIFFRACTIONf_plane_restr0.004271
X-RAY DIFFRACTIONf_dihedral_angle_d7.5621322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5783-1.61780.26881350.25042509264497
1.6178-1.66150.27211300.222425822712100
1.6615-1.71040.19721370.199525742711100
1.7104-1.76560.20221400.18925792719100
1.7656-1.82870.18071330.183125642697100
1.8287-1.90190.17341340.166325602694100
1.9019-1.98850.17431370.173626052742100
1.9885-2.09330.19831320.156125662698100
2.0933-2.22450.17291420.15325972739100
2.2245-2.39620.13561350.150525932728100
2.3962-2.63740.16291370.156526092746100
2.6374-3.01890.13691370.152526062743100
3.0189-3.80330.15321420.135426292771100
3.8033-47.33220.14021450.134827472892100
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)
14.3134-1.5992-1.09863.9751.11471.8961-0.00150.0708-0.0265-0.23270.02-0.09350.05270.0054-0.00130.223-0.0083-0.01190.13320.01260.1425-44.72276.72361.126
22.1626-0.9102-1.62331.58010.65482.38710.06930.23550.0517-0.248-0.05550.0138-0.1053-0.2596-0.01210.2272-0.0137-00.17910.00730.1663-47.434113.9563-2.2325
31.4299-0.40640.39921.909-0.76381.1729-0.0544-0.02380.02780.0117-0.0516-0.2979-0.09020.10180.11080.2153-0.01690.0240.1933-0.01560.2256-34.99326.28696.5728
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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