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- PDB-6dvk: Computationally designed mini tetraloop-tetraloop receptor by the... -

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Basic information

Entry
Database: PDB / ID: 6dvk
TitleComputationally designed mini tetraloop-tetraloop receptor by the RNAMake program - construct 6 (miniTTR 6)
ComponentsRNA (95-MER)
KeywordsRNA / Automated RNA Structure Design / Tetra-loop tetra-loop receptor / RNA motif
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsEiler, D.R. / Yesselman, J.D. / Costantino, D.A. / Das, R. / Kieft, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100953 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112294 United States
CitationJournal: Nat Nanotechnol / Year: 2019
Title: Computational design of three-dimensional RNA structure and function.
Authors: Yesselman, J.D. / Eiler, D. / Carlson, E.D. / Gotrik, M.R. / d'Aquino, A.E. / Ooms, A.N. / Kladwang, W. / Carlson, P.D. / Shi, X. / Costantino, D.A. / Herschlag, D. / Lucks, J.B. / Jewett, M. ...Authors: Yesselman, J.D. / Eiler, D. / Carlson, E.D. / Gotrik, M.R. / d'Aquino, A.E. / Ooms, A.N. / Kladwang, W. / Carlson, P.D. / Shi, X. / Costantino, D.A. / Herschlag, D. / Lucks, J.B. / Jewett, M.C. / Kieft, J.S. / Das, R.
History
DepositionJun 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: RNA (95-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,93410
Polymers30,5771
Non-polymers3579
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)233.372, 25.358, 42.861
Angle α, β, γ (deg.)90.000, 99.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (95-MER)


Mass: 30577.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM sodium cacodylate (pH 5.5), 20 mM MgCl2, 2 mM cobalt hexammine, and 40% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.58954 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.58954 Å / Relative weight: 1
ReflectionResolution: 2.55→115 Å / Num. obs: 8270 / % possible obs: 97.6 % / Redundancy: 3.01 % / Biso Wilson estimate: 39.918 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.176 / Χ2: 0.994 / Net I/σ(I): 6.44 / Num. measured all: 24890 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.622.6040.9031.0314405875530.3391.12794.2
2.62-2.692.9770.9051.1616795935640.4851.09695.1
2.69-2.773.1460.6941.4918976076030.5790.83299.3
2.77-2.853.0160.6191.8616475625460.6880.74597.2
2.85-2.942.9350.382.7715355325230.7930.46298.3
2.94-3.052.8240.2264.1214915365280.9560.27798.5
3.05-3.162.8590.1585.4215015385250.9690.19397.6
3.16-3.292.9540.1396.7414184874800.9770.16898.6
3.29-3.443.1320.1416.9314444694610.9790.16998.3
3.44-3.613.2620.1417.7115434824730.9780.16798.1
3.61-3.83.1630.1188.5113194224170.9850.14198.8
3.8-4.033.1090.1069.2712254053940.9860.12697.3
4.03-4.313.1330.09810.412724114060.9810.11798.8
4.31-4.663.1180.09110.9510823463470.9820.109100
4.66-5.13.1220.08611.6811243713600.9850.10397
5.1-5.73.0530.0712.748702872850.9910.08399.3
5.7-6.582.9830.08111.38532872860.9910.09799.7
6.58-8.063.0680.07912.77182382340.9890.09598.3
8.06-11.42.9340.07214.425341921820.9880.08594.8
11.4-1152.8930.05316.122981191030.9950.06386.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→115 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.88 / SU B: 15.441 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 377 4.6 %RANDOM
Rwork0.2315 ---
obs0.2332 7897 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.91 Å2 / Biso mean: 38.435 Å2 / Biso min: 4.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å2-0 Å2-0.09 Å2
2---0.67 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.55→115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2008 15 2 2025
Biso mean--32.84 5.93 -
Num. residues----95
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0112251
X-RAY DIFFRACTIONr_bond_other_d0.0040.02920
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.293512
X-RAY DIFFRACTIONr_angle_other_deg1.61632236
X-RAY DIFFRACTIONr_chiral_restr0.0950.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021116
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 23 -
Rwork0.349 528 -
all-551 -
obs--93.87 %

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