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- PDB-5wxi: EarP bound with dTDP-rhamnose (soaked) -

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Basic information

Entry
Database: PDB / ID: 5wxi
TitleEarP bound with dTDP-rhamnose (soaked)
ComponentsEarP
KeywordsTRANSFERASE / glycosyltransferase / GT-B / EF-P / rhamnosylation / translation elongation / dTDP-rhamnose
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / Transferases; Glycosyltransferases; Hexosyltransferases / BETA-MERCAPTOETHANOL / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesNeisseria meningitidis serogroup B / serotype 15
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSengoku, T. / Yokoyama, S. / Yanagisawa, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT Japan
AMED Japan
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP
Authors: Sengoku, T. / Suzuki, T. / Dohmae, N. / Watanabe, C. / Honma, T. / Hikida, Y. / Yamaguchi, Y. / Takahashi, H. / Yokoyama, S. / Yanagisawa, T.
History
DepositionJan 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 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

Downloads & links

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Assembly

Deposited unit
A: EarP
B: EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,77018
Polymers88,4402
Non-polymers2,33016
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-132 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.578, 195.388, 46.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EarP


Mass: 44219.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B / serotype 15 (strain H44/76) (bacteria)
Strain: H44/76 / Gene: NMH_0797 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: E6MVV9

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Non-polymers , 5 types, 651 molecules

#2: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes-NaOH buffer (pH 6.8-7.5), 20% PEG3350, 0.2M ammonium sulfate
PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.85 Å / Num. obs: 61063 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.649 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: apo EarP

Resolution: 2→48.847 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.2132 1465 2.4 %
Rwork0.172 --
obs0.173 60983 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6133 0 135 635 6903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066525
X-RAY DIFFRACTIONf_angle_d0.858899
X-RAY DIFFRACTIONf_dihedral_angle_d17.2353809
X-RAY DIFFRACTIONf_chiral_restr0.051929
X-RAY DIFFRACTIONf_plane_restr0.0061137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07160.24141440.23695835X-RAY DIFFRACTION100
2.0716-2.15450.26091450.21675840X-RAY DIFFRACTION100
2.1545-2.25260.24341440.19645890X-RAY DIFFRACTION100
2.2526-2.37130.22161440.18715880X-RAY DIFFRACTION100
2.3713-2.51990.23321460.1865895X-RAY DIFFRACTION100
2.5199-2.71440.21771460.17815934X-RAY DIFFRACTION100
2.7144-2.98760.23871460.17615918X-RAY DIFFRACTION100
2.9876-3.41980.19961470.16215972X-RAY DIFFRACTION100
3.4198-4.30820.19591480.14376058X-RAY DIFFRACTION100
4.3082-48.86150.18941550.15986296X-RAY DIFFRACTION100
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)
10.77320.2608-1.0321.91970.23732.70080.07790.0880.1742-0.00220.02470.0324-0.1112-0.226-0.07960.12580.0233-0.00080.19430.03350.261435.702771.86448.5031
20.8203-0.39340.12762.4273-0.5110.7568-0.0043-0.03440.04080.05050.0397-0.1076-0.01020.0106-0.03490.1392-0.0010.01670.1323-0.00410.16723.424394.1419.8759
31.2626-0.60191.08292.3346-0.5062.42510.16470.1546-0.0387-0.3635-0.19480.27920.0308-0.0050.04940.21780.0519-0.06690.2138-0.02730.26289.088258.29766.1565
41.0465-0.1704-0.08481.31760.50581.08640.0077-0.0119-0.00370.01080.00790.07750.00480.0359-0.01640.1188-0.0178-0.00640.11950.00670.080321.782333.46145.3275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 379 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 140 )
4X-RAY DIFFRACTION4chain 'B' and (resid 141 through 378 )

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