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

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Basic information

Entry
Database: PDB / ID: 4lbv
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 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 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 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)45,97913
Polymers44,6111
Non-polymers1,36812
Water4,468248
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)91,95926
Polymers89,2222
Non-polymers2,73724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5650 Å2
ΔGint-215 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.380, 98.610, 39.780
Angle α, β, γ (deg.)90.000, 95.970, 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 , 6 types, 260 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
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: 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 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.02→32.07 Å / Num. obs: 37060 / % possible obs: 97.6 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.6 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.02-2.070.5332.59250276398
9.03-32.070.02643.3130741388.8

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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: 2.03→28.081 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.21 / σ(F): 1.38 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 1823 5 %
Rwork0.1615 --
obs0.163 36472 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.08 Å2 / Biso mean: 33.1053 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: LAST / Resolution: 2.03→28.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 75 248 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083263
X-RAY DIFFRACTIONf_angle_d1.174461
X-RAY DIFFRACTIONf_chiral_restr0.074507
X-RAY DIFFRACTIONf_plane_restr0.005579
X-RAY DIFFRACTIONf_dihedral_angle_d13.5841196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.08490.26451310.222626612792100
2.0849-2.14620.28121530.209326582811100
2.1462-2.21540.23751480.19226732821100
2.2154-2.29460.22391490.181826122761100
2.2946-2.38640.21321170.169626802797100
2.3864-2.4950.21411250.166326942819100
2.495-2.62640.18261360.171126472783100
2.6264-2.79080.23311300.176626632793100
2.7908-3.00610.22231560.180826602816100
3.0061-3.30820.21221500.171626762826100
3.3082-3.78590.17611410.144326502791100
3.7859-4.7660.13731420.12332670281299
4.766-28.08360.16061450.14882705285099
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)
12.44820.06690.35712.0883-0.02632.2148-0.0762-0.28680.30550.17630.0719-0.0623-0.14080.0035-0.02550.16290.0322-0.00810.1557-0.04550.13841.32072.566150.4676
24.5315-0.79920.38853.81931.11363.8475-0.01740.1384-0.199-0.16240.0889-0.10950.06360.2936-0.03640.13760.0320.03520.19770.03110.156657.0667-17.684441.6552
31.69611.77220.11224.62720.39683.11290.1616-0.4174-0.70340.4079-0.29340.2470.3133-0.22150.07560.3036-0.07840.00170.22060.05360.447530.4492-24.675844.0298
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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