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- PDB-1ha3: ELONGATION FACTOR TU IN COMPLEX WITH aurodox -

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Basic information

Entry
Database: PDB / ID: 1ha3
TitleELONGATION FACTOR TU IN COMPLEX WITH aurodox
ComponentsELONGATION FACTOR TUEF-Tu
KeywordsTRANSLATION / GTPASE / AURODOX / N-METHYL-KIRROMYCIN / ANTIBIOTIC / RIBOSOME
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / RNA 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
BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / N-METHYL KIRROMYCIN / Elongation factor Tu-A / Elongation factor Tu-A
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVogeley, L. / Palm, G.J. / Mesters, J.R. / Hilgenfeld, R.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Conformational Change of Elongation Factor TU Induced by Antibiotic Binding: Crystal Structure of the Complex between EF-TU:Gdp and Aurodox
Authors: Vogeley, L. / Palm, G.J. / Mesters, J.R. / Hilgenfeld, R.
#1: 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. / Hogg, T.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1995
Title: Regulatory Gtpases
Authors: Hilgenfeld, R.
#3: 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.
#4: 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.
History
DepositionMar 26, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
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 / 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.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_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 "D" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "D" 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,13310
Polymers89,4202
Non-polymers2,7138
Water10,773598
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A: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0665
Polymers44,7101
Non-polymers1,3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0665
Polymers44,7101
Non-polymers1,3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.000, 101.400, 79.100
Angle α, β, γ (deg.)90.00, 113.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.981974, -0.188989, -0.003066), (0.188839, 0.980238, 0.058942), (-0.008134, -0.058458, 0.998257)
Vector: -0.85358, 43.67351, -12.77729)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 44709.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TERNARY COMPLEX WITH GUANOSINE DIPHOSPHATE AND AURODOX
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Gene: TUFB / Plasmid: PEFTU10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07157, UniProt: Q5SHN6*PLUS, dGTPase

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Non-polymers , 5 types, 606 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MAU / N-METHYL KIRROMYCIN / AURODOX / 1-METHYLMOCIMYCIN / ANTIBIOTIC X-5108 / GOLDINODOX / GOLDINOMYCIN


Mass: 810.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H62N2O12 / Comment: antibiotic*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.8 Å3/Da / Density % sol: 55 %
Description: DOMAIN 1 AND 2/3 HAD TO BE USED AS SEPARATE SEARCH MODELS
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP METHOD (PROTEIN SOLUTION:WELL 1:1). PROTEIN CONCENTRATION 10 MG/ML. WELL: 50 MM TRIS, 200 MM NAOAC, 23-25% PEG4000, PH 8.0 MOLAR RATIO EF-TU:GDP:AURODOX = 1:1:5
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium acetate1drop
2100 mMammonium sulfate1drop
35 mM1dropMgSO4
40.020 mMGDP1drop
59-12 mg/mlprotein1drop
650 mMTris1reservoir
7200 mMsodium acetate1reservoir
823-25 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.913
DetectorType: X-RAY RESEARCH, HAMBURG, GERMANY / Detector: CCD / Date: Sep 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 67199 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.263 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 287768 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 98.7 % / Num. unique obs: 3322 / Num. measured obs: 9419 / Rmerge(I) obs: 0.263

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EXM

1exm


Resolution: 2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3358 5 %RANDOM
Rwork0.191 ---
obs0.191 66574 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.18 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 182 598 6756
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_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.982.5
X-RAY DIFFRACTIONc_scbond_it2.083
X-RAY DIFFRACTIONc_scangle_it3.095
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2892 331 5 %
Rwork0.2428 5701 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LIGANDS.PARLIGANDS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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