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- PDB-7vnw: Crystal Structure of tRNAVal from Sulfolobus Tokodaii(Dephosphory... -

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Basic information

Entry
Database: PDB / ID: 7vnw
TitleCrystal Structure of tRNAVal from Sulfolobus Tokodaii(Dephosphorylated)
ComponentsRNA (78-MER)
KeywordsRNA / tRNAVal
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsYamashita, S. / Ohira, T. / Suzuki, T. / Tomtia, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
CitationJournal: Nature / Year: 2022
Title: Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Authors: Ohira, T. / Minowa, K. / Sugiyama, K. / Yamashita, S. / Sakaguchi, Y. / Miyauchi, K. / Noguchi, R. / Kaneko, A. / Orita, I. / Fukui, T. / Tomita, K. / Suzuki, T.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2May 25, 2022Group: 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 2.0Jun 15, 2022Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 26, 2023Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / struct_conn
Item: _atom_site.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_PDB_ins_code ..._atom_site.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_PDB_ins_code / _pdbx_poly_seq_scheme.pdb_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code
Revision 3.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (78-MER)
B: RNA (78-MER)


Theoretical massNumber of molelcules
Total (without water)50,6792
Polymers50,6792
Non-polymers00
Water1,20767
1
A: RNA (78-MER)


Theoretical massNumber of molelcules
Total (without water)25,3391
Polymers25,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (78-MER)


Theoretical massNumber of molelcules
Total (without water)25,3391
Polymers25,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.560, 116.680, 56.140
Angle α, β, γ (deg.)90.000, 101.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (78-MER)


Mass: 25339.291 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfurisphaera tokodaii (archaea)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 80mM NaCl, 12mM Speremin-4HCl, 30% MPD, 40mM NaCacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.61→31.92 Å / Num. obs: 12524 / % possible obs: 99.7 % / Redundancy: 6.701 % / Biso Wilson estimate: 50.581 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.121 / Χ2: 0.88 / Net I/σ(I): 14.52 / Num. measured all: 83923 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.61-2.686.3251.1511.889480.5961.25499.6
2.68-2.756.5770.862.678740.7850.93499.3
2.75-2.836.7520.6973.388820.8520.75599.8
2.83-2.926.6530.5354.278550.9080.58100
2.92-3.016.9340.3416.668130.9620.36999.1
3.01-3.126.8810.210.458160.9860.21799.6
3.12-3.246.9740.13614.077730.9940.147100
3.24-3.376.820.12116.167150.9920.13199
3.37-3.526.2910.11616.537220.9910.12799.7
3.52-3.696.8370.09918.276820.9950.10799.7
3.69-3.896.7190.09618.616310.9950.104100
3.89-4.137.0830.08621.056250.9960.09399.4
4.13-4.416.9220.07523.215530.9970.081100
4.41-4.766.7910.06924.635510.9960.07599.8
4.76-5.226.3170.06524.614990.9960.071100
5.22-5.836.4430.05825.934450.9960.06499.1
5.83-6.746.9080.05927.454020.9960.064100
6.74-8.256.6210.0531.163350.9980.054100
8.25-11.676.2320.04432.172630.9960.04899.6
11.67-31.926.5860.03737.571400.9990.0497.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300024972

Resolution: 2.61→31.92 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 627 5.01 %
Rwork0.2236 11894 -
obs0.2255 12521 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.09 Å2 / Biso mean: 51.059 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 2.61→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3360 0 67 3427
Biso mean---38.98 -
Num. residues----156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.61-2.870.38321560.349129653121
2.87-3.290.25581570.23629733130
3.29-4.140.21491560.201729563112
4.14-31.920.27071580.204330003158
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)
11.5380.2595-0.19330.4360.43281.11380.19310.1659-0.0392-0.1775-0.0732-0.1002-0.09990.20550.02990.27730.05030.06710.27690.03210.3779-123.378616.86927.3389
21.49050.7082-0.22751.75820.21861.82240.09570.14310.1063-0.5145-0.04530.0771-0.0756-0.41020.09120.32410.0816-0.01960.36090.02450.4128-133.138649.541426.393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A)A)0
2X-RAY DIFFRACTION2(chain B)B)0

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