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- PDB-1d8t: CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU (EF-TU-MGGDP) COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1d8t
TitleCRYSTAL STRUCTURE OF ELONGATION FACTOR, TU (EF-TU-MGGDP) COMPLEXED WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC
Components
  • ELONGATION FACTOR TUEF-Tu
  • THIOCILLIN GE2270
KeywordsHYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC COMPLEX / THIOPEPTIDE / ANTIBIOTIC / ANTIBACTERIAL / THIAZOLE / OXAZOLE / HYDROLASE / GTPASE / TRANSLATION ELONGATION FACTOR / PROTEIN SYNTHESIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / cytolysis / GTPase activity / defense response to bacterium / response to antibiotic / GTP binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Elongation factor Tu, domain 2 / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu (EF-Tu), GTP-binding domain / Elongation factor Tu C-terminal domain / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation factors / Translation elongation factor EFTu-like, domain 2 ...Elongation factor Tu, domain 2 / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu (EF-Tu), GTP-binding domain / Elongation factor Tu C-terminal domain / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation factors / 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
Elongation factor Tu 1 / Elongation factor Tu 1 / GE2270a / ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / Thiocillin GE2270
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
PLANOBISPORA ROSEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsHeffron, S.E. / Jurnak, F.
CitationJournal: Biochemistry / Year: 2000
Title: Structure of an EF-TU Complex with a Thiazolyl Peptide Antibiotic Determined at 2.35 A Resolution: Atomic Basis for Ge2270A Inhibition of EF-TU.
Authors: Heffron, S.E. / Jurnak, F.
History
DepositionOct 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Apr 18, 2012Group: Structure summary
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.7Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELONGATION FACTOR TU
B: ELONGATION FACTOR TU
C: THIOCILLIN GE2270
D: THIOCILLIN GE2270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,09438
Polymers89,3884
Non-polymers2,70634
Water6,828379
1
A: ELONGATION FACTOR TU
C: THIOCILLIN GE2270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28323
Polymers44,6942
Non-polymers1,58921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-38.2 kcal/mol
Surface area17610 Å2
MethodPISA
2
B: ELONGATION FACTOR TU
D: THIOCILLIN GE2270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,81115
Polymers44,6942
Non-polymers1,11713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-34.7 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)133.470, 45.170, 144.000
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2007-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein ELONGATION FACTOR TU / EF-Tu / EF-TU


Mass: 43209.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE47*PLUS
#2: Protein/peptide THIOCILLIN GE2270 / GE2270A


Type: Thiopeptide / Class: Antibiotic / Mass: 1484.681 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: GEA2270A IS A THIOPEPTIDE CONSISTING OF ONE PYRIDINE, ONE OXAZOLE AND FIVE THIAZOLE RINGS. THE OBSERVED C-TERMINAL AMINO GROUP NH2(15) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED ...Details: GEA2270A IS A THIOPEPTIDE CONSISTING OF ONE PYRIDINE, ONE OXAZOLE AND FIVE THIAZOLE RINGS. THE OBSERVED C-TERMINAL AMINO GROUP NH2(15) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE.
Source: (natural) PLANOBISPORA ROSEA (bacteria) / References: UniProt: Q7M0J8, GE2270a

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Non-polymers , 4 types, 413 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical...
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsGEA2270A is a member of a sulphur-rich heterocyclic peptides class. All members share a macrocylic ...GEA2270A is a member of a sulphur-rich heterocyclic peptides class. All members share a macrocylic core, consisting of a nitrogen containing, six-membered ring central to dehydroamino acids and a subset of five member ring structures including thiazoles, thiazolines and oxazoles. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha- carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. In addition cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain produce a pyridinyl ring. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. Several isomers are produced. The structural differences between them lie in the extent of the modifications, methylation, methoxylation, and oxidation of the thiazole and oxazole rings, and methylation of asparagine. The amidation of Pro-14 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growpH: 7.6
Details: TRIS-HCL, MAGNESIUM CHLORIDE, GDP, POLYETHYLENE GLYCOL 3350, AMMONIUM ACETATE, AMMONIUM CITRATE, PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.4 mg/mlprotein1drop
220 %(w/v)PEG33501drop
30.2 Mammonium acetate1drop
40.1 Mammonium citrate1drop
550 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→24.44 Å / Num. obs: 31214 / % possible obs: 86.3 % / Observed criterion σ(I): -4 / Redundancy: 1.8 % / Biso Wilson estimate: 29.75 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 16.4
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.108 / % possible all: 60.7
Reflection
*PLUS
Num. measured all: 55193
Reflection shell
*PLUS
% possible obs: 60.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNSrefinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementResolution: 2.35→24.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1817617.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: SOME NCS RESTRAINTS WERE APPLIED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2178 7 %RANDOM
Rwork0.2 ---
obs0.2 31214 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.13 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--4.79 Å20 Å2-0.54 Å2
2--8.08 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.35→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 178 379 6713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 314 7.4 %
Rwork0.226 3923 -
obs--71.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4GDP96_CNS.PARAMGDP96_CNS.TOP
X-RAY DIFFRACTION5PARAM_ED6.GETOPH_ED5.GE
X-RAY DIFFRACTION6ACETATE.PARAMACETATE.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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