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- PDB-2hdn: Trypsin-modified Elongation Factor Tu in complex with tetracyclin... -

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Basic information

Entry
Database: PDB / ID: 2hdn
TitleTrypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution
Components(Elongation factor EF- ...) x 2
KeywordsTRANSLATION / trypsin-modified EF-Tu / GTPase center / complex with tetracycline
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / 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
GUANOSINE-5'-DIPHOSPHATE / TETRACYCLINE / Elongation factor Tu 1 / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMui, S. / Heffron, S.E. / Aorora, A. / Abel, K. / Bergmann, E. / Jurnak, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.
Authors: Heffron, S.E. / Mui, S. / Aorora, A. / Abel, K. / Bergmann, E. / Jurnak, F.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_conn / struct_ref_seq_dif / 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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor EF-Tu
B: Elongation factor EF-Tu
C: Elongation factor EF-Tu
D: Elongation factor EF-Tu
E: Elongation factor EF-Tu
F: Elongation factor EF-Tu
G: Elongation factor EF-Tu
H: Elongation factor EF-Tu
I: Elongation factor EF-Tu
J: Elongation factor EF-Tu
K: Elongation factor EF-Tu
L: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,86130
Polymers244,38912
Non-polymers5,47218
Water4,396244
1
A: Elongation factor EF-Tu
B: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-40 kcal/mol
Surface area16720 Å2
MethodPISA
2
C: Elongation factor EF-Tu
D: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-40 kcal/mol
Surface area16770 Å2
MethodPISA
3
E: Elongation factor EF-Tu
F: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-40 kcal/mol
Surface area16790 Å2
MethodPISA
4
G: Elongation factor EF-Tu
H: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-39 kcal/mol
Surface area16850 Å2
MethodPISA
5
I: Elongation factor EF-Tu
J: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-41 kcal/mol
Surface area16790 Å2
MethodPISA
6
K: Elongation factor EF-Tu
L: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6445
Polymers40,7322
Non-polymers9123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-41 kcal/mol
Surface area16600 Å2
MethodPISA
7
A: Elongation factor EF-Tu
B: Elongation factor EF-Tu
C: Elongation factor EF-Tu
D: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,28710
Polymers81,4634
Non-polymers1,8246
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-86 kcal/mol
Surface area30250 Å2
MethodPISA
8
I: Elongation factor EF-Tu
J: Elongation factor EF-Tu
K: Elongation factor EF-Tu
L: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,28710
Polymers81,4634
Non-polymers1,8246
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-86 kcal/mol
Surface area29940 Å2
MethodPISA
9
E: Elongation factor EF-Tu
F: Elongation factor EF-Tu
G: Elongation factor EF-Tu
H: Elongation factor EF-Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,28710
Polymers81,4634
Non-polymers1,8246
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-85 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.710, 156.060, 134.830
Angle α, β, γ (deg.)90.000, 95.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Elongation factor EF- ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Elongation factor EF-Tu


Mass: 3765.300 Da / Num. of mol.: 6 / Fragment: EF-Tu fragment, residues 8-44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: tufA / References: UniProt: P0A6N1, UniProt: P0CE47*PLUS
#2: Protein
Elongation factor EF-Tu


Mass: 36966.277 Da / Num. of mol.: 6 / Fragment: EF-Tu fragment, residues 59-393 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: tufA / References: UniProt: P0A6N1, UniProt: P0CE47*PLUS

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Non-polymers , 4 types, 262 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-TAC / TETRACYCLINE / Tetracycline


Mass: 444.435 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H24N2O8 / Comment: medication, antibiotic*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 6

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.4 %
Crystal growMethod: vapor diffusion, sitting drop
Details: Multiple crystals were used to collect the native and each derivative data set. VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→47.3 Å / Num. obs: 73085 / % possible obs: 92.3 % / Rmerge(I) obs: 0.099

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an unrefined 2.7 Angstrom model of E. coli trypsin-modified EF-Tu-MgGDP, consisting of residues 9 to 40, 50 to 258 and 260 to 393, plus one Mg ion and GDP

Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Each molecular replacement solution was verified by successfully cross-phasing the mercury derivative sites with the generated model phases.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4601 6.5 %random
Rwork0.18 ---
obs-64651 91.6 %-
Solvent computationBsol: 40.313 Å2
Displacement parametersBiso mean: 44.966 Å2
Baniso -1Baniso -2Baniso -3
1-6.585 Å20 Å2-7.172 Å2
2---1.468 Å20 Å2
3----5.117 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16998 0 366 244 17608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.7811.5
X-RAY DIFFRACTIONc_mcangle_it4.3662
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.82
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2MYTOPPAR:gdp96_cns.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4MYTOPPAR:tac_cns5.param
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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