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- PDB-8ym3: Structural basis of Elongation factor Tu in regulating photoinhib... -

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Basic information

Entry
Database: PDB / ID: 8ym3
TitleStructural basis of Elongation factor Tu in regulating photoinhibition in Synechococcus sp. PCC 7942.
ComponentsElongation factor Tu
KeywordsPHOTOSYNTHESIS / Elongation factor / cyanobacteria PCC 7942 / photosystem 2 / photoremediation
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 / 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, 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 / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCheng, C. / Ma, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271358 China
CitationJournal: To Be Published
Title: Structural basis of Elongation factor Tu in regulating photoinhibition in Synechococcus sp. PCC 7942.
Authors: Chen, C. / Ma, H.
History
DepositionMar 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9217
Polymers44,1131
Non-polymers8086
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.897, 86.548, 60.775
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elongation factor Tu / EF-Tu


Mass: 44113.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence reference for (strain ATCC 33912 / PCC 7942 / FACHB-805) is not available in Uniprot at the time of biocuration. Current sequence reference is from Uniprot id P18668.
Source: (gene. exp.) Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Gene: tuf, tufA, syc0656_d / Production host: Escherichia coli (E. coli) / References: UniProt: P18668

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Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 61.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.085 M HEPES sodium pH 7.5, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.05→42.71 Å / Num. obs: 35495 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.909 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.16 / Rrim(I) all: 0.403 / Χ2: 0.79 / Net I/σ(I): 5
Reflection shellResolution: 2.05→2.1 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.758 / Num. measured all: 17421 / Num. unique obs: 2637 / CC1/2: 0.283 / Rpim(I) all: 0.756 / Rrim(I) all: 1.919 / Χ2: 0.78 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42.71 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1774 5.01 %
Rwork0.185 --
obs0.1869 35391 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 1 448 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123203
X-RAY DIFFRACTIONf_angle_d1.4584338
X-RAY DIFFRACTIONf_dihedral_angle_d17.3791194
X-RAY DIFFRACTIONf_chiral_restr0.074500
X-RAY DIFFRACTIONf_plane_restr0.009563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.26781210.23222407X-RAY DIFFRACTION92
2.1-2.160.27551400.22382573X-RAY DIFFRACTION100
2.16-2.230.24811300.22872557X-RAY DIFFRACTION99
2.23-2.310.24511420.22192599X-RAY DIFFRACTION100
2.31-2.410.25551430.21132586X-RAY DIFFRACTION100
2.41-2.520.27441330.21652599X-RAY DIFFRACTION100
2.52-2.650.23761470.20522567X-RAY DIFFRACTION100
2.65-2.810.22361350.18562573X-RAY DIFFRACTION100
2.81-3.030.24921400.18622641X-RAY DIFFRACTION100
3.03-3.340.19441450.17122587X-RAY DIFFRACTION100
3.34-3.820.20211360.1582612X-RAY DIFFRACTION100
3.82-4.810.1591310.13842645X-RAY DIFFRACTION100
4.81-42.710.21121310.17442671X-RAY DIFFRACTION100

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