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- PDB-1exm: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS ELONGATION FACTOR TU (E... -

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Basic information

Entry
Database: PDB / ID: 1exm
TitleCRYSTAL STRUCTURE OF THERMUS THERMOPHILUS ELONGATION FACTOR TU (EF-TU) IN COMPLEX WITH THE GTP ANALOGUE GPPNHP.
ComponentsELONGATION FACTOR TU (EF-TU)
KeywordsTRANSLATION / GTPASE / MOLECULAR SWITCH / TRNA / RIBOSOME / Q-BETA REPLICASE / CHAPERONE / DISULFIDE ISOMERASE
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Elongation factor Tu-A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHogg, T. / Mesters, J.R. / Hilgenfeld, R.
Citation
Journal: The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions
Year: 2000
Title: Insights into the GTPase Mechanism of EF-Tu from Structural Studies
Authors: Hilgenfeld, R. / Mesters, J.R. / Hogg, T.
#1: Journal: Nature / Year: 1993
Title: Crystal structure of active elongation factor Tu reveals major domain rearrangements
Authors: Berchtold, H. / Reshetnikova, L. / Reiser, C.O.A. / Schirmer, N.K. / Sprinzl, M. / Hilgenfeld, R.
#2: Journal: J.Cryst.Growth / Year: 1992
Title: Crystals of intact elongation factor Tu from Thermus thermophilus diffracting to 1.45 Angstrom resolution.
Authors: Reshetnikova, L. / Schirmer, N.K. / Reiser, C.O.A. / Berchtold, H. / Storm, R. / Hilgenfeld, R. / Sprinzl, M.
#3: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1995
Title: REGULATORY GTPASES
Authors: HILGENFELD, R.
History
DepositionMay 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Feb 7, 2024Group: Advisory / Data collection ...Advisory / 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 / 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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELONGATION FACTOR TU (EF-TU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2563
Polymers44,7101
Non-polymers5472
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.500, 99.500, 40.200
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

21A-621-

HOH

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Components

#1: Protein ELONGATION FACTOR TU (EF-TU) / EF-TU


Mass: 44709.887 Da / Num. of mol.: 1 / Fragment: INTACT WILD-TYPE EF-TU / Source method: isolated from a natural source
Details: BINARY COMPLEX WITH GUANOSINE-5'-(BETA,GAMMA-IMIDO) TRIPHOSPHATE (GPPNHP)
Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60338
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 18.015 Da / Num. of mol.: 252 / 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: 8

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mM Sodium cacodylate, 5mM Magnesium sulfate, 38-44% Ammonium sulfate, 7-10 mg/mL EF-Tu, molar ratio EF-Tu:GppNHp = 1:5, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODEELLIOTT GX-2111.5418
SYNCHROTRONSRS PX9.620.87
Detector
TypeIDDetector
ENRAF-NONIUS FAST1DIFFRACTOMETER
ENRAF-NONIUS FAST2DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.871
ReflectionNum. all: 47681 / Biso Wilson estimate: 21.2 Å2
Reflection shellResolution: 1.7→1.81 Å / Num. unique all: 4693 / % possible all: 43.7

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementResolution: 1.7→14.78 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2172 4.6 %RANDOM
Rwork0.209 ---
obs0.209 47681 73.7 %-
all-49853 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.19 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å20 Å21.07 Å2
2---4.87 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 33 252 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.312.5
X-RAY DIFFRACTIONc_scbond_it3.623
X-RAY DIFFRACTIONc_scangle_it5.235
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 205 4.4 %
Rwork0.331 4488 -
obs--43.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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