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- PDB-5w75: Crystal Structure of Reconstructed Bacterial Elongation Factor No... -

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Basic information

Entry
Database: PDB / ID: 5w75
TitleCrystal Structure of Reconstructed Bacterial Elongation Factor Node 168
ComponentsElongation factor TuEF-Tu
KeywordsTRANSLATION / ancestral gene reconstruction / thermostability / EF-Tu / ASR
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsOrtlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
W. M. Keck Foundation United States
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
B: Elongation factor Tu
C: Elongation factor Tu
D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,92837
Polymers174,6714
Non-polymers5,25733
Water11,746652
1
A: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3275
Polymers43,6681
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,05410
Polymers43,6681
Non-polymers1,3869
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39611
Polymers43,6681
Non-polymers1,72810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,15011
Polymers43,6681
Non-polymers1,48210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.417, 173.420, 208.178
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 / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Elongation factor Tu / EF-Tu / EF-Tu


Mass: 43667.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E) (bacteria)
Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: tuf, CTN_0991 / Production host: Escherichia coli (E. coli) / References: UniProt: B9K884
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 681 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.35 M ammonium sulfate and 0.1 M HEPES pH 7.5 / Temp details: 23 degrees C

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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: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 145229 / % possible obs: 98.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.081 / Χ2: 1.651 / Net I/σ(I): 13.2 / Num. measured all: 858145
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.385.60.47136411.202193.5
2.38-2.485.60.368140091.263195.7
2.48-2.595.60.299142521.324197.8
2.59-2.735.70.222144751.49198.9
2.73-2.95.90.168145941.683199.5
2.9-3.126.10.121146531.866199.8
3.12-3.446.20.091146932.3199.8
3.44-3.936.20.073147812.281199.8
3.93-4.956.10.066148651.595199.8
4.95-406.10.046152661.324199.4

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Processing

Software
NameVersionClassification
REFMACrefinement
SERGUIdata collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.298→29.705 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1995 1.38 %
Rwork0.1937 --
obs0.1941 144724 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.83 Å2 / Biso mean: 46.221 Å2 / Biso min: 22.67 Å2
Refinement stepCycle: final / Resolution: 2.298→29.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12060 0 313 652 13025
Biso mean--70.54 50.57 -
Num. residues----1543
Refinement TLS params.Method: refined / Origin x: 24.456 Å / Origin y: 2.954 Å / Origin z: -46.801 Å
111213212223313233
T0.3083 Å20.0001 Å20.0013 Å2-0.2731 Å20.0066 Å2--0.275 Å2
L0.2068 °2-0.0287 °2-0.085 °2-0.0223 °20.069 °2--0.0909 °2
S-0.0064 Å °0.045 Å °-0.0008 Å °0.0042 Å °-0.0144 Å °-0.0018 Å °0.011 Å °-0.0106 Å °0.0217 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 395
2X-RAY DIFFRACTION1B9 - 395
3X-RAY DIFFRACTION1C9 - 395
4X-RAY DIFFRACTION1D9 - 395
5X-RAY DIFFRACTION1A401 - 402
6X-RAY DIFFRACTION1A504 - 556
7X-RAY DIFFRACTION1B401 - 402
8X-RAY DIFFRACTION1B511 - 540
9X-RAY DIFFRACTION1C401 - 402
10X-RAY DIFFRACTION1C502 - 551
11X-RAY DIFFRACTION1D401 - 402
12X-RAY DIFFRACTION1D513 - 567
13X-RAY DIFFRACTION1A403 - 404
14X-RAY DIFFRACTION1B403 - 408
15X-RAY DIFFRACTION1C403 - 408
16X-RAY DIFFRACTION1D403 - 409
17X-RAY DIFFRACTION1D410
18X-RAY DIFFRACTION1C409
19X-RAY DIFFRACTION1C410
20X-RAY DIFFRACTION1B409

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