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- PDB-6s8z: Elongation Factor P from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 6s8z
TitleElongation Factor P from Corynebacterium glutamicum
ComponentsElongation factor P
KeywordsTRANSLATION / Elongation Factor P
Function / homology
Function and homology information


translation elongation factor activity / cytoplasm
Similarity search - Function
Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / 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 ...Translation elongation factor P/YeiP, conserved site / Elongation factor P signature. / Translation elongation factor P/YeiP, central / Translation elongation factor P / 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 / Translation elongation factor, KOW-like / Elongation factor P (EF-P) KOW-like domain / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Elongation factor P / Elongation factor P
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchneider, S. / Scheidler, C.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK2062 Germany
CitationJournal: Cell Rep / Year: 2020
Title: Structure and Function of an Elongation Factor P Subfamily in Actinobacteria.
Authors: Pinheiro, B. / Scheidler, C.M. / Kielkowski, P. / Schmid, M. / Forne, I. / Ye, S. / Reiling, N. / Takano, E. / Imhof, A. / Sieber, S.A. / Schneider, S. / Jung, K.
History
DepositionJul 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: 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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9276
Polymers20,6651
Non-polymers2625
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.201, 38.163, 55.356
Angle α, β, γ (deg.)90.000, 93.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 20665.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: efp, CS176_1554 / Production host: Corynebacterium glutamicum (bacteria) / References: UniProt: A0A1B4WLR4, UniProt: Q45288*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium acetate 0.1 M HEPES pH 7.5 22 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.2→38.58 Å / Num. obs: 10932 / % possible obs: 98.6 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.065 / Rrim(I) all: 0.145 / Net I/σ(I): 7.98
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.1 % / Rmerge(I) obs: 2.355 / Mean I/σ(I) obs: 0.63 / Num. unique obs: 1081 / CC1/2: 0.613 / Rpim(I) all: 1.158 / Rrim(I) all: 2.631 / % possible all: 98.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OYY

3oyy


Resolution: 2.2→38.58 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.265 --546
Rwork0.206 ---
obs-10928 98.6 %-
Displacement parametersBiso mean: 30.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 17 56 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131475
X-RAY DIFFRACTIONf_angle_d1.7211989
X-RAY DIFFRACTIONf_chiral_restr0.0971225
X-RAY DIFFRACTIONf_plane_restr0.0053263
X-RAY DIFFRACTIONf_dihedral_angle_d13.253875

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