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- PDB-2bvn: E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa -

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Basic information

Entry
Database: PDB / ID: 2bvn
TitleE. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa
ComponentsELONGATION FACTOR TUEF-Tu
KeywordsELONGATION FACTOR / TRANSLATION / GTPASE / ANTIBIOTIC / GTP-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / 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
ENACYLOXIN IIA / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Elongation factor Tu 1 / Elongation factor Tu 2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsParmeggiani, A. / Krab, I.M. / Watanabe, T. / Nielsen, R.C. / Dahlberg, C. / Nyborg, J. / Nissen, P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics.
Authors: Parmeggiani, A. / Krab, I.M. / Watanabe, T. / Nielsen, R.C. / Dahlberg, C. / Nyborg, J. / Nissen, P.
History
DepositionJun 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" 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. THE SHEETS PRESENTED AS "BD" 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. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELONGATION FACTOR TU
B: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9778
Polymers86,4792
Non-polymers2,4986
Water3,261181
1
A: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4884
Polymers43,2391
Non-polymers1,2493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4884
Polymers43,2391
Non-polymers1,2493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.070, 72.070, 335.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.50038, -0.8658, 0.0029), (0.8658, -0.50038, 0.00042), (0.00109, 0.00272, 1)
Vector: -0.22612, -0.61432, -0.07002)

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Components

#1: Protein ELONGATION FACTOR TU / EF-Tu / EF-TU / P-43


Mass: 43239.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli
References: UniProt: P0A6N1, UniProt: P0CE48*PLUS, EC: 3.6.1.48
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ENX / ENACYLOXIN IIA


Mass: 702.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H45Cl2NO11
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2 MICROL PROTEIN SOLUTION MIXED WITH 1 MICROL RESERVOIR SOLUTION (450 MM NACL. 22% PEG6000, 6% GLYCEROL, 7 MM MGCL2, 100 MM TRIS-HCL PH 7.5), SITTING DROP 19 DEG. C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 37737 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 53.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OB2

1ob2


Resolution: 2.3→29.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3463299.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1510 4 %RANDOM
Rwork0.23 ---
obs0.23 37612 99.8 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 33.7032 Å2 / ksol: 0.313266 e/Å3
Displacement parametersBiso mean: 49.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.04 Å20 Å20 Å2
2--6.04 Å20 Å2
3----12.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 160 181 6078
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_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.371.5
X-RAY DIFFRACTIONc_mcangle_it4.852
X-RAY DIFFRACTIONc_scbond_it5.282
X-RAY DIFFRACTIONc_scangle_it7.132.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.43 53 4.5 %
Rwork0.367 1133 -
obs--100 %

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