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- PDB-4h9g: Probing EF-Tu with a very small brominated fragment library ident... -

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Basic information

Entry
Database: PDB / ID: 4h9g
TitleProbing EF-Tu with a very small brominated fragment library identifies the CCA pocket
ComponentsElongation factor Tu-A
KeywordsTRANSLATION / P-loop / GTPase / GTP Binding / tRNA Binding / Ribosome Binding
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP 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
5-bromofuran-2-carboxylic acid / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / AMMONIUM ION / Elongation factor Tu-A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGroftehauge, M.K. / Therkelsen, M. / Taaning, R.H. / Skrydstrup, T. / Morth, J.P. / Nissen, P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Identifying ligand-binding hot spots in proteins using brominated fragments.
Authors: Grftehauge, M.K. / Therkelsen, M.O. / Taaning, R. / Skrydstrup, T. / Morth, J.P. / Nissen, P.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2Feb 28, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20613
Polymers44,6821
Non-polymers1,52412
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.205, 98.627, 39.751
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elongation factor Tu-A / EF-Tu-A


Mass: 44681.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tuf, tufA / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60338, protein-synthesizing GTPase

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Non-polymers , 6 types, 394 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-14J / 5-bromofuran-2-carboxylic acid


Mass: 190.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H3BrO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1.8M ammonium sulfate, 15% sucrose, 0.1M tris, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009
RadiationMonochromator: Si (111) double crystal monochromator, first crystal indirectly water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.852→29.39 Å / Num. all: 178052 / Redundancy: 2.01 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 0.1391 / Mean I/σ(I) obs: 1.17 / % possible all: 91.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→29.39 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic with TLS / σ(F): 1.35 / Phase error: 18.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 2121 5.01 %
Rwork0.1543 --
obs0.1558 42355 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6464 Å20 Å20.4069 Å2
2--1.3367 Å2-0 Å2
3----2.9831 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 83 382 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073548
X-RAY DIFFRACTIONf_angle_d1.1574875
X-RAY DIFFRACTIONf_dihedral_angle_d14.3581349
X-RAY DIFFRACTIONf_chiral_restr0.075544
X-RAY DIFFRACTIONf_plane_restr0.005646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.97490.2541430.23272666X-RAY DIFFRACTION100
1.9749-2.02430.27621380.21182636X-RAY DIFFRACTION100
2.0243-2.0790.2361410.18662702X-RAY DIFFRACTION100
2.079-2.14020.23321420.19132669X-RAY DIFFRACTION100
2.1402-2.20930.23661400.1712685X-RAY DIFFRACTION100
2.2093-2.28820.18211400.16552659X-RAY DIFFRACTION100
2.2882-2.37980.21471410.16032683X-RAY DIFFRACTION100
2.3798-2.48810.19841430.15862702X-RAY DIFFRACTION100
2.4881-2.61920.19321400.15582668X-RAY DIFFRACTION100
2.6192-2.78320.18961420.15482667X-RAY DIFFRACTION100
2.7832-2.9980.16171400.15712676X-RAY DIFFRACTION100
2.998-3.29950.18791440.15282727X-RAY DIFFRACTION100
3.2995-3.77630.1671390.13542655X-RAY DIFFRACTION100
3.7763-4.75560.13551430.11962715X-RAY DIFFRACTION100
4.7556-33.34920.17111450.15072724X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1828-0.03940.24151.8296-0.12922.142-0.0533-0.23160.24620.1420.0377-0.0851-0.15110.0411-0.00730.15310.0233-0.00420.1403-0.03690.1189-28.28382.165510.4344
23.0535-1.1065-0.54382.27760.99323.3357-0.06570.0908-0.1079-0.08850.0447-0.13350.06230.38750.02310.12970.02760.0330.24110.03720.1469-12.673-16.60992.674
31.30920.78840.48631.68350.45940.98770.0458-0.3819-0.6550.2536-0.08840.38430.2248-0.18890.01570.268-0.03110.03490.1790.06550.4046-37.1383-25.57554.3689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 209 )
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 405 )

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