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- PDB-6n6c: Vibrio cholerae Oligoribonuclease bound to pAA -

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Basic information

Entry
Database: PDB / ID: 6n6c
TitleVibrio cholerae Oligoribonuclease bound to pAA
Components
  • RNA (5'-R(P*AP*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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.619 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*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5913
Polymers21,5682
Non-polymers231
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-21 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.375, 89.375, 59.451
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 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, VC0395_A2743, VC395_0384 / Plasmid: pET28a / 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*AP*A)-3')


Mass: 613.454 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.: 267 / 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: 3.18 Å3/Da / Density % sol: 61.3 %
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 22, 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: 1.619→47.148 Å / Num. obs: 35203 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 26.32 Å2 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Rsym value: 0.047 / Net I/av σ(I): 10.9 / Net I/σ(I): 28.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.62-1.7111.31.060.750510.3261.111.0699.3
1.71-1.8112.10.6431.247980.1920.6710.643100
1.81-1.9311.90.3382.345500.1020.3540.338100
1.93-2.0912.20.1784.442290.0530.1860.178100
2.09-2.2912.40.0977.939340.0290.1010.097100
2.29-2.5612.20.06311.935170.0190.0650.063100
2.56-2.9612.30.041731390.0120.0420.04100
2.96-3.6212.10.02820.526750.0080.030.028100
3.62-5.1211.90.02423.821000.0070.0250.024100
5.12-47.14811.40.02323.612100.0070.0240.02399.9

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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: 1.619→24.75 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.85
RfactorNum. reflection% reflection
Rfree0.1546 1762 5.01 %
Rwork0.1461 --
obs0.1466 35163 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.17 Å2 / Biso mean: 32.5809 Å2 / Biso min: 18.11 Å2
Refinement stepCycle: final / Resolution: 1.619→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 45 1 268 1783
Biso mean--24.65 46.6 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061573
X-RAY DIFFRACTIONf_angle_d0.8162142
X-RAY DIFFRACTIONf_chiral_restr0.054239
X-RAY DIFFRACTIONf_plane_restr0.004267
X-RAY DIFFRACTIONf_dihedral_angle_d7.5661310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6189-1.66260.28411290.25632502263198
1.6626-1.71160.24361390.211725512690100
1.7116-1.76680.21981320.201525292661100
1.7668-1.82990.18041330.175525472680100
1.8299-1.90320.18331340.164725572691100
1.9032-1.98970.19081340.165825662700100
1.9897-2.09460.19111310.15125482679100
2.0946-2.22570.14161390.142325562695100
2.2257-2.39750.13821360.140825602696100
2.3975-2.63850.15981350.15325772712100
2.6385-3.01970.141350.144726012736100
3.0197-3.80230.15871400.130925972737100
3.8023-24.75290.13021450.135327102855100
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)
13.7555-1.0576-1.10043.20990.9111.8944-0.09360.087-0.1132-0.24790.0526-0.16280.09850.04160.06820.287-0.01480.01560.1707-0.00350.2065-43.76356.25440.7995
22.1893-0.6003-1.46331.66510.43332.2912-0.00310.260.0221-0.28390.00240.0175-0.0603-0.221-0.00470.2562-0.0197-0.0020.19290.00090.1753-47.518313.8842-2.1769
31.6618-0.47390.4381.5521-0.90951.4255-0.0601-0.0492-0.03460.0383-0.0778-0.3169-0.09650.14270.15830.2643-0.0230.02630.2165-0.01430.2752-35.22866.19126.5781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:23)A1 - 23
2X-RAY DIFFRACTION2(chain A and resid 24:99)A24 - 99
3X-RAY DIFFRACTION3(chain A and resid 100:181)A100 - 181

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