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Basic information

Entry
Database: PDB / ID: 4lbw
TitleIdentifying ligand binding hot spots in proteins using brominated fragments
ComponentsElongation factor Tu-A
KeywordsPROTEIN BINDING / GTPase / PLANT PROTEIN
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: 1.741 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)45,94412
Polymers44,6111
Non-polymers1,33311
Water6,089338
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)91,88824
Polymers89,2222
Non-polymers2,66622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5440 Å2
ΔGint-192 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.220, 98.490, 39.700
Angle α, β, γ (deg.)90.00, 95.68, 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: 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, 349 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.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 61.68 %
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: 1.74→30.81 Å / Num. obs: 57511 / % possible obs: 97.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.6
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2 / Num. measured all: 16042 / Num. unique all: 4234 / % possible all: 98.7

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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: 1.741→30.81 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 2918 5.07 %
Rwork0.1705 --
obs0.1717 57508 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.06 Å2 / Biso mean: 38.0354 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: LAST / Resolution: 1.741→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 74 338 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073283
X-RAY DIFFRACTIONf_angle_d1.1454493
X-RAY DIFFRACTIONf_chiral_restr0.074509
X-RAY DIFFRACTIONf_plane_restr0.005585
X-RAY DIFFRACTIONf_dihedral_angle_d12.8061205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7409-1.76950.29951570.268225662723100
1.7695-1.80.29181370.240726042741100
1.8-1.83270.2631190.230525732692100
1.8327-1.86790.25011280.218926022730100
1.8679-1.90610.22591510.220925832734100
1.9061-1.94750.23781230.203625882711100
1.9475-1.99280.23811260.200126342760100
1.9928-2.04260.21461520.193225862738100
2.0426-2.09780.25291320.189926172749100
2.0978-2.15950.23411340.184725652699100
2.1595-2.22920.2211210.184926332754100
2.2292-2.30890.20031460.174625992745100
2.3089-2.40130.22341420.174625702712100
2.4013-2.51050.19341460.173126032749100
2.5105-2.64280.19861370.17326212758100
2.6428-2.80830.18351450.172925912736100
2.8083-3.0250.21471530.179725912744100
3.025-3.3290.18381400.172126042744100
3.329-3.810.16451410.14925922733100
3.81-4.79730.14511370.130326182755100
4.7973-30.81980.18211510.1612650280199
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)
13.2851-0.29190.74022.2156-0.14212.5359-0.1175-0.52120.38190.210.0943-0.1182-0.182-0.0885-0.02550.18910.0530.00030.2197-0.08280.150941.49742.86150.1395
24.0359-1.4065-0.31323.62651.4243.765-0.0394-0.066-0.1671-0.12130.0609-0.13290.06220.385-0.00590.15690.03050.0370.24420.05140.16657.168-16.273142.4675
31.77241.51030.70251.96660.61531.10720.2324-0.8028-1.00940.3581-0.15270.46730.3535-0.3273-0.07410.358-0.09720.00620.3030.15950.609132.4957-24.805143.8357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 209 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 302 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 405 )A0

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