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- PDB-8s8u: Escherichia coli translation elongation factor P like protein (EfpL) -

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Basic information

Entry
Database: PDB / ID: 8s8u
TitleEscherichia coli translation elongation factor P like protein (EfpL)
ComponentsElongation factor P-like protein
KeywordsTRANSLATION / EF-P like / YeiP / Polyproline translation
Function / homology
Function and homology information


peptide biosynthetic process / translation elongation factor activity / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor P-like, YeiP / Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor, KOW-like / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal ...Translation elongation factor P-like, YeiP / Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor, KOW-like / Elongation factor P, C-terminal / Translation elongation factor P/YeiP / Elongation factor P (EF-P) OB domain / Elongation factor P, C-terminal / Elongation factor P, C-terminal / Elongation factor P (EF-P) OB domain / Elongation factor P (EF-P) KOW-like domain / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Elongation factor P-like protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDhamotharan, K. / von Ehr, J. / Schlundt, A. / Lassak, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences.
Authors: Sieber, A. / Parr, M. / von Ehr, J. / Dhamotharan, K. / Kielkowski, P. / Brewer, T. / Schapers, A. / Krafczyk, R. / Qi, F. / Schlundt, A. / Frishman, D. / Lassak, J.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor P-like protein
B: Elongation factor P-like protein


Theoretical massNumber of molelcules
Total (without water)43,0272
Polymers43,0272
Non-polymers00
Water1,11762
1
A: Elongation factor P-like protein


Theoretical massNumber of molelcules
Total (without water)21,5131
Polymers21,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor P-like protein


Theoretical massNumber of molelcules
Total (without water)21,5131
Polymers21,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.526, 53.341, 64.76
Angle α, β, γ (deg.)90, 102.74, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elongation factor P-like protein


Mass: 21513.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: yeiP, b2171, JW5362 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6N8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Sodium-HEPES 20% PEG 8000 10 mM Hexaamminecobalt (III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.60832 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60832 Å / Relative weight: 1
ReflectionResolution: 2.27→63.16 Å / Num. obs: 18764 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.06-63.165.40.04529.53290.9960.030.0550.9698.6
2.27-2.346217220.8520.40411.1199.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
BUSTER2.10.4refinement
PDB-REDO8.06refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
MxCuBEv2data collection
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→59.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.368 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.252
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 958 -RANDOM
Rwork0.2457 ---
obs0.2473 18621 98.8 %-
Displacement parametersBiso mean: 63.57 Å2
Baniso -1Baniso -2Baniso -3
1--7.3727 Å20 Å23.6117 Å2
2--4.8399 Å20 Å2
3---2.5329 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.27→59.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 62 3027
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073018HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.894081HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1085SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3018HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion394SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1986SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion15.1
LS refinement shellResolution: 2.27→2.29 Å
RfactorNum. reflection% reflection
Rfree0.3348 19 -
Rwork0.3571 --
obs0.3561 397 93.98 %
Refinement TLS params.

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)
10.6138-0.61740.79760.2662-0.17611.3331-0.18150.0537-0.20470.05370.1344-0.2489-0.2047-0.24890.04710.16050.0791-0.0044-0.11460.0302-0.084313.7691-0.35926.558
21.69660.66830.14460.5606-0.37020.3213-0.180.0630.03760.0630.1709-0.07930.0376-0.07930.0091-0.0175-0.0205-0.004-0.03840.01070.016320.34451.31390.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 188
2X-RAY DIFFRACTION2{ B|* }B1 - 188

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