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- PDB-1gax: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE C... -

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Basic information

Entry
Database: PDB / ID: 1gax
TitleCRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
Components
  • TRNA(VAL)
  • VALYL-TRNA SYNTHETASE
KeywordsLIGASE/RNA / protein-RNA complex / Rossmann fold / coiled coil / tRNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


valine-tRNA ligase / valine-tRNA ligase activity / valyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Valyl-trna Synthetase; Chain: A, domain 4 / Valyl-trna Synthetase; Chain: A, domain 4 - #10 / Valyl-tRNA synthetase, C-terminal domain / Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain ...Valyl-trna Synthetase; Chain: A, domain 4 / Valyl-trna Synthetase; Chain: A, domain 4 - #10 / Valyl-tRNA synthetase, C-terminal domain / Valine-tRNA ligase / Valyl-tRNA synthetase, tRNA-binding arm / Valyl tRNA synthetase, anticodon-binding domain / Valyl tRNA synthetase tRNA binding arm / Valyl-tRNA synthetase, tRNA-binding arm superfamily / Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Isoleucyl-tRNA Synthetase; Domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE / RNA / RNA (> 10) / Valine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsFukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Tao, J. / Vassylyev, D.G. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.
Authors: Fukai, S. / Nureki, O. / Sekine, S. / Shimada, A. / Tao, J. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionJun 23, 2000Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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 / struct_site
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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: TRNA(VAL)
D: TRNA(VAL)
A: VALYL-TRNA SYNTHETASE
B: VALYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,32810
Polymers246,1784
Non-polymers1,1516
Water2,846158
1
C: TRNA(VAL)
A: VALYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6645
Polymers123,0892
Non-polymers5753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: TRNA(VAL)
B: VALYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6645
Polymers123,0892
Non-polymers5753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)411.810, 411.810, 81.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Cell settingtetragonal
Space group name H-MP42212

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Components

#1: RNA chain TRNA(VAL)


Mass: 24174.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: sequence from Thermus thermophilus
#2: Protein VALYL-TRNA SYNTHETASE / E.C.6.1.1.9 / VALRS


Mass: 98914.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PK7 / Production host: Escherichia coli (E. coli) / References: UniProt: P96142, valine-tRNA ligase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-VAA / N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE


Mass: 444.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N8O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, sodium cacodylate, magnesium sulfate, 1,8-diaminooctane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
21,8-diaminooctane11
3MgSO411
4(NH4)2SO411
5MgSO412
6(NH4)2SO412
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
250 mMsodium cacodylate1drop
31.0 Mammonium sulfate1drop
410 mMmagnesium sulfate1drop
56 %1,8-diaminooctane1drop
650 mMsodium cacodylate1reservoir
72.8 Mammonium sulfate1reservoir
810 mMmagnesium sulfate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 151446 / Num. obs: 151446 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6
Reflection shellResolution: 2.89→2.94 Å / Rmerge(I) obs: 0.328 / Num. unique all: 6672 / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 551728
Reflection shell
*PLUS
% possible obs: 85.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 7492 5 %RANDOM
Rwork0.2447 ---
all-150205 --
obs-150205 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13940 3206 64 158 17368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_impr_deg1.121
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.272 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12

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