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- PDB-7kju: Cgi121-tRNA complex -

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Basic information

Entry
Database: PDB / ID: 7kju
TitleCgi121-tRNA complex
ComponentsRNA (75-MER)
KeywordsRNA / KEOPS / tRNA / Cgi121 / RNA modifying enzyme / N6-threonylcarbamoyl adenosine
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å
AuthorsCeccarelli, D.F. / Beenstock, J. / Wan, L.C.K. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 143277 Canada
CitationJournal: Nat Commun / Year: 2020
Title: A substrate binding model for the KEOPS tRNA modifying complex.
Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / ...Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / Schriemer, D.C. / Bayfield, M.A. / Durocher, D. / Sicheri, F.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5115
Polymers24,4131
Non-polymers974
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-32 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.493, 168.527, 68.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: RNA chain RNA (75-MER)


Mass: 24413.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pUC19 / Details (production host): hepatitis delta virus ribozyme
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 6626255
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 5.98 Å3/Da / Density % sol: 79.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 0.2 M zinc acetate, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97964 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 3.1→49.14 Å / Num. obs: 10895 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.025 / Rrim(I) all: 0.085 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.11-3.198.90.93170167920.9560.330.9892.1100
13.91-49.149.50.03612111270.9990.0120.03836.887.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.11 Å49.03 Å
Translation3.11 Å49.03 Å

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Processing

Software
NameVersionClassification
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L0U

3l0u


Resolution: 3.102→49.034 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 603 5.6 %
Rwork0.2481 10162 -
obs0.2492 10765 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 432.37 Å2 / Biso mean: 181.6269 Å2 / Biso min: 37.96 Å2
Refinement stepCycle: final / Resolution: 3.102→49.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1594 4 0 1598
Biso mean--108.37 --
Num. residues----75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1022-3.41440.30071460.3211240094
3.4144-3.90820.33431510.2801251399
3.9082-4.92320.26881310.26972595100
4.9232-49.030.24991750.2235265499
Refinement TLS params.Method: refined / Origin x: -32.618 Å / Origin y: -10.6402 Å / Origin z: 10.417 Å
111213212223313233
T0.5461 Å20.2847 Å2-0.0825 Å2-0.638 Å20.0735 Å2--0.6952 Å2
L1.3117 °2-0.3082 °2-0.6091 °2-0.9064 °2-0.5988 °2--0.9442 °2
S0.1168 Å °-0.9014 Å °-0.0359 Å °0.5265 Å °-0.0912 Å °-0.5753 Å °-0.0741 Å °0.6813 Å °-0.0862 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 75)

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