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- PDB-5wxj: Apo EarP -

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Basic information

Entry
Database: PDB / ID: 5wxj
TitleApo EarP
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 / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesNeisseria meningitidis serogroup B / serotype 15
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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)89,89718
Polymers88,4402
Non-polymers1,45716
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-148 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.622, 195.774, 46.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes-NaOH buffer (pH 6.8-7.5), 20% PEG3350, and 0.2 M ammonium sulfate
PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48.94 Å / Num. obs: 77019 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / CC1/2: 0.704 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata extraction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→47.361 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 1846 2.4 %
Rwork0.1583 --
obs0.1592 77019 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→47.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 78 724 6889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176391
X-RAY DIFFRACTIONf_angle_d1.3638706
X-RAY DIFFRACTIONf_dihedral_angle_d5.2945153
X-RAY DIFFRACTIONf_chiral_restr0.101904
X-RAY DIFFRACTIONf_plane_restr0.011121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31741370.2485660X-RAY DIFFRACTION100
1.9-1.95590.24771400.20215718X-RAY DIFFRACTION100
1.9559-2.01910.25821420.19215724X-RAY DIFFRACTION100
2.0191-2.09120.24441400.1765693X-RAY DIFFRACTION100
2.0912-2.1750.19691400.15945717X-RAY DIFFRACTION100
2.175-2.2740.18681400.15125702X-RAY DIFFRACTION100
2.274-2.39380.18581410.15055762X-RAY DIFFRACTION100
2.3938-2.54380.21261420.1625761X-RAY DIFFRACTION100
2.5438-2.74020.2191430.15745779X-RAY DIFFRACTION100
2.7402-3.01590.2241420.16655774X-RAY DIFFRACTION100
3.0159-3.45220.18841430.15295832X-RAY DIFFRACTION100
3.4522-4.3490.16421450.13165899X-RAY DIFFRACTION100
4.349-47.37670.17181510.15556152X-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)
11.9075-0.4233-0.3433.36470.21113.78660.06120.0990.2683-0.16780.06070.0915-0.2188-0.1528-0.01050.12220.01170.04070.16970.03650.27838.834875.59225.5046
20.4251-0.2336-0.08594.36531.91261.989-0.05570.02180.10760.2460.0728-0.10640.1474-0.1095-0.0010.14680.0099-0.0090.18550.01280.227932.786270.854617.6648
31.2828-0.14050.34693.3268-1.37521.9008-0.02260.09450.0399-0.11660.078-0.1520.0131-0.0177-0.05530.17120.01260.050.1529-0.00880.184623.485100.32714.254
42.6938-1.48070.25352.6215-0.08731.08080.0069-0.21380.00150.24350.09880.1266-0.0652-0.0906-0.09330.1876-0.00650.05550.1450.04040.146919.910487.961527.0538
51.2883-0.42730.29943.5471-0.08183.7920.13340.10640.0132-0.3964-0.05070.13680.1620.0134-0.07290.17490.0495-0.05510.2431-0.00870.20966.167658.23693.4388
60.6132-0.1946-0.00041.17480.53290.7768-0.01540.00280.0291-0.0002-0.00240.0767-0.0132-0.00240.01880.1396-0.0152-0.00320.15040.0050.101721.489236.15466.9156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 290 )
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 379 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 378 )

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