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- PDB-5w7q: Crystal Structure of Reconstructed Bacterial Elongation Factor No... -

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Basic information

Entry
Database: PDB / ID: 5w7q
TitleCrystal Structure of Reconstructed Bacterial Elongation Factor Node 168
ComponentsConsensus Elongation Factor
KeywordsTRANSLATION / ancestral gene reconstruction / thermostability / EF-Tu / ASR
Function / homologyTranslation factors / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsOrtlund, E.A.
CitationJournal: Structure / Year: 2018
Title: Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.
Authors: Okafor, C.D. / Pathak, M.C. / Fagan, C.E. / Bauer, N.C. / Cole, M.F. / Gaucher, E.A. / Ortlund, E.A.
History
DepositionJun 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Consensus Elongation Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3833
Polymers40,9161
Non-polymers4682
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.476, 104.046, 43.833
Angle α, β, γ (deg.)90.000, 111.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Consensus Elongation Factor


Mass: 40915.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% Peg 10K, 100mM Na Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10877 / % possible obs: 92.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.05 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.841 / Net I/σ(I): 9.7 / Num. measured all: 47115
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.5-2.543.90.4351.349182.4
2.54-2.594.10.4291.348187.9
2.59-2.643.90.4131.348188.2
2.64-2.694.10.3551.287190.5
2.69-2.754.30.3031.401191.2
2.75-2.824.20.271.347192.2
2.82-2.894.30.2521.414193.5
2.89-2.964.30.2241.44195.8
2.96-3.054.40.1891.454194.8
3.05-3.154.50.1661.578193.9
3.15-3.264.40.1261.713196.4
3.26-3.394.50.1171.825194.2
3.39-3.554.50.0971.765195.6
3.55-3.734.50.0921.805193.7
3.73-3.974.50.0772.037194.5
3.97-4.274.40.0652.162193.2
4.27-4.74.50.0542.187193.7
4.7-5.384.60.062.378192.2
5.38-6.784.50.0712.435191.3
6.78-504.20.0664.213190

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.5→30.537 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.24
RfactorNum. reflection% reflection
Rfree0.2472 751 6.92 %
Rwork0.1966 --
obs0.2002 10858 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.01 Å2 / Biso mean: 53.4183 Å2 / Biso min: 18.47 Å2
Refinement stepCycle: final / Resolution: 2.5→30.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 39 27 2918
Biso mean--39.83 34.37 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032930
X-RAY DIFFRACTIONf_angle_d0.6233975
X-RAY DIFFRACTIONf_chiral_restr0.048458
X-RAY DIFFRACTIONf_plane_restr0.003515
X-RAY DIFFRACTIONf_dihedral_angle_d18.2521769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.494-2.68650.35181430.26921856199985
2.6865-2.95660.29791460.24382055220193
2.9566-3.3840.29891550.21342088224395
3.384-4.26160.25831580.18172048220694
4.2616-30.53960.17031490.16532060220992
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)
12.70510.2917-0.25261.95720.74681.48120.11540.11330.2774-0.0207-0.02950.5092-0.1772-0.183-0.09220.29340.03710.03370.20270.00360.3384-7.077510.97379.3445
22.2910.1242-1.22022.0239-1.62681.93850.09730.33660.328-0.0133-0.04140.01230.2942-0.1248-0.00630.2716-0.0018-0.03630.30620.06770.31894.813510.28890.1755
33.21960.14771.08562.9830.35342.442-0.04540.1787-0.34070.0490.02480.13060.34430.0722-0.02350.32950.02630.03570.20670.00140.21542.1749-3.33716.6558
40.95260.8270.12921.53510.590.5746-0.1049-0.2017-0.08280.2270.15480.595-0.12040.0115-0.06090.33650.05090.00880.3701-0.01690.37049.977533.713918.6113
50.97560.61640.88073.21642.69134.6069-0.0950.02490.0842-0.1623-0.0076-0.0169-0.26460.0650.08620.1697-0.00480.0020.25090.02130.251314.342232.59173.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 84 )A8 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 126 )A85 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 199 )A127 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 225 )A200 - 225
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 393 )A226 - 393

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