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- PDB-7vnv: Crystal Structure of tRNAVal from Sulfolobus Tokodaii -

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Basic information

Entry
Database: PDB / ID: 7vnv
TitleCrystal Structure of tRNAVal from Sulfolobus Tokodaii
ComponentsRNA (78-MER)
KeywordsRNA / tRNAVal
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 3.1Nov 29, 2023Group: 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)50,9032
Polymers50,9032
Non-polymers00
Water1,65792
1
A: RNA (78-MER)


Theoretical massNumber of molelcules
Total (without water)25,4511
Polymers25,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (78-MER)


Theoretical massNumber of molelcules
Total (without water)25,4511
Polymers25,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.650, 116.620, 57.238
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (78-MER)


Mass: 25451.400 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.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.47 %
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: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→32.05 Å / Num. obs: 32418 / % possible obs: 98.7 % / Redundancy: 6.719 % / Biso Wilson estimate: 47.227 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 0.843 / Net I/σ(I): 15.65 / Num. measured all: 217828 / Scaling rejects: 4
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
1.9-1.956.7641.5991.5315719240023240.6021.73196.8
1.95-2.016.6191.2481.9715362235423210.6711.35598.6
2.01-2.076.5920.9142.6814866230522550.7890.99297.8
2.07-2.137.020.7943.4115303220621800.8510.85798.8
2.13-2.26.9960.5854.5115132220221630.9270.63298.2
2.2-2.286.9190.4495.9114060205420320.9610.48598.9
2.28-2.366.8260.3637.113706204320080.9660.39398.3
2.36-2.466.5470.2828.5612511192919110.9750.30799.1
2.46-2.576.7960.21910.9712606187218550.9860.23799.1
2.57-2.697.2040.16914.0112758178417710.9910.18299.3
2.69-2.847.0930.11618.1411881169416750.9950.12598.9
2.84-3.016.8240.07624.3411136164416320.9970.08299.3
3.01-3.226.2640.04931.679127146014570.9980.05499.8
3.22-3.486.3760.04436.558927141514000.9980.04898.9
3.48-3.816.6450.04238.468712131813110.9980.04599.5
3.81-4.266.6520.03840.377690116411560.9980.04299.3
4.26-4.926.1280.03940.26312103810300.9990.04299.2
4.92-6.026.4270.03742.3156758838830.9990.041100
6.02-8.526.0040.03742.1740836886800.9980.0498.8
8.52-32.056.0480.03243.6322623793740.9980.03598.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IVS

1ivs


Resolution: 1.9→32.05 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 1621 5 %
Rwork0.1947 --
obs0.1959 32415 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3368 0 92 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073754
X-RAY DIFFRACTIONf_angle_d1.0135842
X-RAY DIFFRACTIONf_dihedral_angle_d13.7461872
X-RAY DIFFRACTIONf_chiral_restr0.047766
X-RAY DIFFRACTIONf_plane_restr0.007162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.33271300.31552470X-RAY DIFFRACTION97
1.96-2.020.30391340.28722554X-RAY DIFFRACTION98
2.02-2.10.31091340.26862547X-RAY DIFFRACTION98
2.1-2.180.3041360.26622574X-RAY DIFFRACTION98
2.18-2.280.32561340.25582546X-RAY DIFFRACTION99
2.28-2.40.29251340.26382550X-RAY DIFFRACTION99
2.4-2.550.30451350.26422574X-RAY DIFFRACTION99
2.55-2.750.32161370.27272594X-RAY DIFFRACTION99
2.75-3.020.26671350.24452575X-RAY DIFFRACTION99
3.02-3.460.20141360.17722566X-RAY DIFFRACTION99
3.46-4.360.17091370.15172617X-RAY DIFFRACTION99
4.36-32.050.15781390.13872627X-RAY DIFFRACTION99
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)
12.4940.0735-0.39481.21490.55281.10160.14370.227-0.0077-0.2841-0.0501-0.1106-0.11650.1194-0.08740.36680.0334-0.01610.20980.02840.2464-123.407716.710627.6467
22.1630.37630.71252.65280.02862.32290.09440.11540.0774-0.3417-0.01230.02820.1167-0.272-0.07780.30930.01320.00420.20080.0110.2712-133.32249.637427.287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:76)
2X-RAY DIFFRACTION2(chain B and resid 1:76)

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