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- PDB-2c77: EF-Tu complexed with a GTP analog and the antibiotic GE2270 A -

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Basic information

Entry
Database: PDB / ID: 2c77
TitleEF-Tu complexed with a GTP analog and the antibiotic GE2270 A
Components
  • ELONGATION FACTOR TU-B
  • 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


translation elongation factor activity / killing of cells of another organism / defense response to bacterium / GTPase activity / GTP binding / extracellular region / cytoplasm
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
GE2270a / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / DI(HYDROXYETHYL)ETHER / Elongation factor Tu-B / Thiocillin GE2270
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
PLANOBISPORA ROSEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsParmeggiani, A. / Krab, I.M. / Okamura, S. / Nielsen, R.C. / Nyborg, J. / Nissen, P.
CitationJournal: Biochemistry / Year: 2006
Title: Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu.
Authors: Parmeggiani, A. / Krab, I.M. / Okamura, S. / Nielsen, R.C. / Nyborg, J. / Nissen, P.
History
DepositionNov 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" 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
B: THIOCILLIN GE2270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8635
Polymers46,2112
Non-polymers6533
Water6,666370
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-20.5 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.320, 94.580, 104.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 44725.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TUFA GENE / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60339, dGTPase
#2: Protein/peptide THIOCILLIN GE2270 / GE22700A


Type: Thiopeptide / Class: Antibiotic / Mass: 1484.681 Da / Num. of mol.: 1 / 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, 373 molecules

#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsGEA2270A IS A MEMBER OF A CLASS OF SULPHUR-RICH HETEROCYCLIC PEPTIDES. ALL MEMBERS SHARE A ...GEA2270A IS A MEMBER OF A CLASS OF SULPHUR-RICH HETEROCYCLIC PEPTIDES. 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. GROUP: 1 NAME: GEA2270A CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 15 DESCRIPTION: 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.

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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 %
Description: DATA WERE LIMITED TO 1.6 A RESOLUTION DUE TO A POWDER RING IN THE DIFFRACTION PATTERN. MR PHASES WERE EXTENDED FROM 03 TO 1.6 A RESOLUTION BY SOLVENT FLIPPING
Crystal growpH: 7 / Details: 18-23% PEG6000, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8133
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8133 Å / Relative weight: 1
ReflectionResolution: 1.6→46 Å / Num. obs: 57292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFT

1eft


Resolution: 1.6→45.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1741200.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD MLF
Details: N-TERMINAL REGION IS INVOLVED IN CRYSTAL PACKING AND ADOPTS AN UNUSUAL STRUCTURE. N-TERMINAL RESIDUE IS DISORDERED AND HAS NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1702 3 %RANDOM
Rwork0.188 ---
obs0.188 57219 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8859 Å2 / ksol: 0.327596 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2---0.94 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 40 370 3635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.752.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.229 179 3.3 %
Rwork0.229 5286 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLIGANDS2.TOP
X-RAY DIFFRACTION3LIGANDS2.PARMG.TOP
X-RAY DIFFRACTION4MG.PARWATER.TOP

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