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- PDB-5xvr: EarP bound with dTDP-rhamnose (co-crystal) -

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Basic information

Entry
Database: PDB / ID: 5xvr
TitleEarP bound with dTDP-rhamnose (co-crystal)
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 / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesNeisseria meningitidis H44/76 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.63 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
DepositionJun 28, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)90,4659
Polymers88,8882
Non-polymers1,5777
Water17,114950
1
A: EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2815
Polymers44,4441
Non-polymers8374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1854
Polymers44,4441
Non-polymers7403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-24 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.390, 195.190, 46.320
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: 44444.234 Da / Num. of mol.: 2 / Mutation: D20N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis H44/76 (bacteria)
Strain: H44/76 / Gene: NMH_0797 / Plasmid: plasmid / Details (production host): pET28c / Production host: Escherichia coli (E. coli) / References: UniProt: E6MVV9
#2: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8% tacsimate pH 6.0, 12% PEG6000, 0.2M lithium sulfate, 10mM dTDP-rhamnose

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→48.8 Å / Num. obs: 110150 / % possible obs: 99.1 % / Redundancy: 21.6 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.63→48.798 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.1999 2603 2.37 %
Rwork0.1643 --
obs0.1652 110028 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.63→48.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 95 950 7208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116554
X-RAY DIFFRACTIONf_angle_d1.128970
X-RAY DIFFRACTIONf_dihedral_angle_d7.3685260
X-RAY DIFFRACTIONf_chiral_restr0.071940
X-RAY DIFFRACTIONf_plane_restr0.0071154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65960.32841320.28975547X-RAY DIFFRACTION98
1.6596-1.69160.28681230.26585483X-RAY DIFFRACTION98
1.6916-1.72610.26351160.23915577X-RAY DIFFRACTION98
1.7261-1.76360.28661340.2185523X-RAY DIFFRACTION98
1.7636-1.80470.24491450.20395551X-RAY DIFFRACTION98
1.8047-1.84980.21311320.18945593X-RAY DIFFRACTION99
1.8498-1.89980.24441370.18785532X-RAY DIFFRACTION98
1.8998-1.95570.2291390.1745593X-RAY DIFFRACTION99
1.9557-2.01880.25111390.17615629X-RAY DIFFRACTION99
2.0188-2.0910.20861370.16335587X-RAY DIFFRACTION99
2.091-2.17470.21581390.16025630X-RAY DIFFRACTION99
2.1747-2.27370.18651400.15365641X-RAY DIFFRACTION99
2.2737-2.39360.18711350.15865676X-RAY DIFFRACTION99
2.3936-2.54350.20061370.16855672X-RAY DIFFRACTION99
2.5435-2.73990.18421410.16945717X-RAY DIFFRACTION100
2.7399-3.01560.24441410.17095710X-RAY DIFFRACTION100
3.0156-3.45180.19171420.15955794X-RAY DIFFRACTION100
3.4518-4.34850.16651440.13655862X-RAY DIFFRACTION100
4.3485-48.81940.17271500.15056108X-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)
11.7424-0.1919-0.41242.54510.01082.2770.09420.050.2605-0.09060.06290.0464-0.1202-0.1053-0.11410.13860.01090.04380.1661-0.00790.249638.315673.60246.1723
21.67792.54390.68978.08150.98381.68730.0472-0.05410.21780.22830.0717-0.26880.0239-0.0017-0.13110.16480.03680.02260.1819-0.02860.270831.061674.49421.58
30.892-0.34350.10641.9458-0.23650.43540.0383-0.03210.17460.07680.0773-0.068-0.08910.0069-0.11310.20110.00660.06240.1522-0.01930.272122.026895.070619.0905
42.2519-0.31251.03984.15020.42923.13140.10780.1628-0.0323-0.341-0.00710.0660.0708-0.019-0.09750.15080.032-0.02530.19110.00320.20566.007457.93463.2974
50.6861-0.181-0.07341.08090.48580.7778-0.0119-0.0289-0.01350.0443-0.01850.0980.01-0.01580.03290.1363-0.0076-0.00410.13680.00260.129221.300936.10886.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 379 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 378 )

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