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- PDB-5nv8: Structural basis for EarP-mediated arginine glycosylation of tran... -

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Basic information

Entry
Database: PDB / ID: 5nv8
TitleStructural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P
ComponentsEF-P arginine 32 rhamnosyl-transferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.294 Å
AuthorsMacosek, J. / Krafczyk, R. / Jagtap, P.K.A. / Lassaka, J. / Hennig, J.
CitationJournal: MBio / Year: 2017
Title: Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P.
Authors: Krafczyk, R. / Macosek, J. / Jagtap, P.K.A. / Gast, D. / Wunder, S. / Mitra, P. / Jha, A.K. / Rohr, J. / Hoffmann-Roder, A. / Jung, K. / Hennig, J. / Lassak, J.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2017Group: Structure summary / Category: audit_author
Revision 1.3May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: EF-P arginine 32 rhamnosyl-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2272
Polymers43,6781
Non-polymers5481
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.680, 131.680, 46.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein EF-P arginine 32 rhamnosyl-transferase


Mass: 43678.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: earP, PP_1857 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88LS1
#2: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M ammonium acetate, 0.1M bis-tris and 27% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.298→46.542 Å / Num. obs: 17539 / % possible obs: 97.13 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.185 / Χ2: 0.976 / Net I/σ(I): 7.73
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1760 / CC1/2: 0.68 / Rrim(I) all: 0.929 / % possible all: 98.49

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.294→46.556 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3394 877 5 %
Rwork0.2893 --
obs0.292 17538 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.294→46.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 35 210 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032394
X-RAY DIFFRACTIONf_angle_d0.6643262
X-RAY DIFFRACTIONf_dihedral_angle_d6.2061886
X-RAY DIFFRACTIONf_chiral_restr0.041362
X-RAY DIFFRACTIONf_plane_restr0.005417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2942-2.43790.37771490.34472834X-RAY DIFFRACTION99
2.4379-2.62620.38821440.33122750X-RAY DIFFRACTION98
2.6262-2.89040.36821480.30282799X-RAY DIFFRACTION98
2.8904-3.30860.33021480.29182809X-RAY DIFFRACTION98
3.3086-4.1680.35311440.26242751X-RAY DIFFRACTION97
4.168-46.56550.30081440.27732718X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / 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)
10.35641.0370.30192.83650.89172.8115-0.04240.9064-0.8315-0.8421-0.91320.6270.1459-0.5503-0.80840.48890.0674-0.09470.4132-0.49050.428762.314826.958410.181
20.611-0.24880.67273.13911.17631.78710.45070.5497-0.7167-0.3494-0.1803-0.12280.22980.0704-0.11270.33990.0936-0.08550.331-0.09920.518865.868520.1037.4661
34.0326-2.632-1.1012.71930.31390.577-0.01380.281-0.3042-0.0203-0.16660.43180.1742-0.08830.09340.2782-0.015-0.03320.2236-0.04960.380149.315140.499421.3155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 377 )

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