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- PDB-4lc0: Identifying ligand binding hot spots in proteins using brominated... -

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Basic information

Entry
Database: PDB / ID: 4lc0
TitleIdentifying ligand binding hot spots in proteins using brominated fragments
ComponentsElongation factor Tu-A
KeywordsPROTEIN BINDING / GTPase
Function / homology
Function and homology information


protein-synthesizing GTPase / translation elongation factor activity / GTPase activity / GTP binding / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / AMMONIUM ION / Elongation factor Tu-A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.221 Å
AuthorsGroftehauge, M.K. / Therkelsen, M. / Taaning, R. / 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
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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_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)45,84811
Polymers44,6111
Non-polymers1,23710
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Elongation factor Tu-A
hetero molecules

A: Elongation factor Tu-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,69522
Polymers89,2222
Non-polymers2,47420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5240 Å2
ΔGint-176 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.830, 98.440, 39.700
Angle α, β, γ (deg.)90.000, 95.790, 90.000
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: 44610.758 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

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Non-polymers , 5 types, 204 molecules

#2: 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
#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


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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→30.81 Å / Num. obs: 27508 / % possible obs: 90.3 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.22-2.281.40.2375.86115186174.2
9.93-30.811.60.05428.1102431086.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
PHASER2.5.4phasing
PHENIXdev_1370refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4H9G

4h9g


Resolution: 2.221→30.805 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1383 5.03 %
Rwork0.1607 --
obs0.1627 27508 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.89 Å2 / Biso mean: 39.8059 Å2 / Biso min: 14.68 Å2
Refinement stepCycle: LAST / Resolution: 2.221→30.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 69 194 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083249
X-RAY DIFFRACTIONf_angle_d1.1594433
X-RAY DIFFRACTIONf_chiral_restr0.073502
X-RAY DIFFRACTIONf_plane_restr0.005574
X-RAY DIFFRACTIONf_dihedral_angle_d13.8651198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2212-2.30060.28141200.23222466258694
2.3006-2.39260.2471350.18526072742100
2.3926-2.50150.22571460.177326052751100
2.5015-2.63330.24731390.1826442783100
2.6333-2.79820.2441040.191526392743100
2.7982-3.01410.26271440.194726242768100
3.0141-3.31710.2331490.176526142763100
3.3171-3.79630.19641250.153826362761100
3.7963-4.78010.15281760.121226092785100
4.7801-30.80820.15851450.137126812826100
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)
12.9365-0.43770.48852.1398-0.21932.1815-0.1525-0.50730.33470.21580.141-0.1029-0.1719-0.0716-0.01360.23160.06470.00220.2681-0.07230.168941.54462.651550.3886
25.449-0.62660.74455.10471.12864.4030.00420.014-0.3578-0.1588-0.041-0.08190.11260.22530.04760.14780.050.05480.23350.04190.206456.8089-17.738341.7807
30.61791.69730.48274.99440.56292.26630.2094-0.5676-0.95010.285-0.19820.22250.2303-0.2369-0.0340.3117-0.06910.00010.28460.12730.616430.2251-24.625943.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 214 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 312 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 405 )A0

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