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- PDB-5w76: Crystal Structure of Reconstructed Bacterial Elongation Factor No... -

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Basic information

Entry
Database: PDB / ID: 5w76
TitleCrystal Structure of Reconstructed Bacterial Elongation Factor Node 168
ComponentsAncestral Elogation Factor N153
KeywordsTRANSLATION / ancestral gene reconstruction / thermostability / EF-Tu / ASR
Function / homology
Function and homology information


Translation 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.152 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 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral Elogation Factor N153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2797
Polymers42,3531
Non-polymers9266
Water2,054114
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)57.326, 73.357, 114.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ancestral Elogation Factor N153


Mass: 42353.141 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)

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Non-polymers , 6 types, 120 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 40% PEG 200 and 0.1 M HEPES pH 7.0

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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: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 23511 / % possible obs: 87.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.73 / Net I/σ(I): 18.8 / Num. measured all: 124793
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.15-2.2340.2231.382165.6
2.23-2.324.70.2081.384171.2
2.32-2.4250.1921.386175.5
2.42-2.555.20.1661.466180.3
2.55-2.715.40.1481.584185.5
2.71-2.925.30.1191.72193.4
2.92-3.215.60.1011.989199.6
3.21-3.685.80.0762.31199.9
3.68-4.635.80.0711.902199.9
4.63-505.50.0681.556199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.152→35.447 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2234 1157 4.93 %
Rwork0.1904 --
obs0.192 23445 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.13 Å2 / Biso mean: 55.1746 Å2 / Biso min: 25.02 Å2
Refinement stepCycle: final / Resolution: 2.152→35.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 102 114 3179
Biso mean--58.58 48.92 -
Num. residues----384
Refinement TLS params.Method: refined / Origin x: 1.696 Å / Origin y: -3.736 Å / Origin z: -26.622 Å
111213212223313233
T0.2898 Å2-0.0147 Å20.003 Å2-0.2546 Å2-0.0083 Å2--0.2884 Å2
L0.9348 °2-0.0739 °2-0.6446 °2-0.5203 °20.2252 °2--1.5448 °2
S-0.0185 Å °0.0578 Å °-0.0419 Å °-0.0031 Å °-0.047 Å °0.081 Å °0.0253 Å °-0.0323 Å °0.0461 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 394
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A402
4X-RAY DIFFRACTION1A501 - 614
5X-RAY DIFFRACTION1A403
6X-RAY DIFFRACTION1A404
7X-RAY DIFFRACTION1A405 - 406

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