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- PDB-1b23: E. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:G... -

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Basic information

Entry
Database: PDB / ID: 1b23
TitleE. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:GTP ternary complex
Components
  • CYSTEINYL TRNA
  • ELONGATION FACTOR TU
KeywordsGENE REGULATION/RNA / TRANSLATION ELONGATION FACTOR / TRANSFER RNA / PROTEIN SYNTHESIS / GENE REGULATION-RNA COMPLEX
Function / homology
Function and homology information


protein-synthesizing GTPase / translation elongation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / Elongation factor Tu
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNissen, P. / Kjeldgaard, M. / Thirup, S. / Nyborg, J.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.
Authors: Nissen, P. / Thirup, S. / Kjeldgaard, M. / Nyborg, J.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of the Ternary Complex of Phe-tRNAphe, EF-TU, and a GTP Analog
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J.
History
DepositionDec 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: CYSTEINYL TRNA
P: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5799
Polymers68,6702
Non-polymers9087
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.750, 132.980, 154.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Cell settingorthorhombic
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11R-179-

MG

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Components

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RNA chain / Protein , 2 types, 2 molecules RP

#1: RNA chain CYSTEINYL TRNA / CYS-TRNA


Mass: 23927.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AMINOACYL LINK BETWEEN A76 AND CYS77 / Source: (gene. exp.) Escherichia coli (E. coli)
#2: Protein ELONGATION FACTOR TU / EF-TU


Mass: 44742.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: YT-1 / Gene: TUFA / Production host: Escherichia coli (E. coli) / References: UniProt: Q01698

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Non-polymers , 5 types, 268 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.34 Å3/Da / Density % sol: 43 % / Description: ANISOTROPIC DIFFRACTION
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.1 M (NH4)2SO4, 30 MM TRIS, 5 MM MES, 10 MM MGCL2, 10 MM DTT, 1 MM GDPNP PH 6.7, 4 DEG. C, HANGING DROP, vapor diffusion - hanging drop, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2TRIS11
3MES11
4MGCL211
5DTT11
6GDPNP11
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.02-2.06 Mammonium sulfate1reservoir
21
31
41
51
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.098
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 18435 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 11.8
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.396 / % possible all: 56
Reflection
*PLUS
Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 56 % / Rmerge(I) obs: 0.396

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTT

1ttt


Resolution: 2.6→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC SCALING WAS CRUCIAL FOR REFINEMENT. ANISOTROPIC SCALEFACTORS DERIVED FROM 4.0 - 2.6 A AMPLITUDES THE ISOPENTENYL GROUP OF MIA R 37 AND THE N-TERMINAL ALA P 1 RESIDUE WERE STEREOCHEMICALLY MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1424 6 %RANDOM
Rwork0.206 ---
obs0.206 18043 89 %-
all-18043 --
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1--31.5 Å20 Å20 Å2
2---4 Å20 Å2
3---14.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.556 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 1590 51 261 5046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d5.41
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52
X-RAY DIFFRACTIONx_mcangle_it2.53
X-RAY DIFFRACTIONx_scbond_it2.54
X-RAY DIFFRACTIONx_scangle_it5.35
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.398 107 4.9 %
Rwork0.362 1314 -
obs--57.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TRNA-MULTI-ENDO.PARAMTRNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3GTP.PARAMGTP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg5.41

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