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- PDB-5wxk: EarP bound with domain I of EF-P -

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Basic information

Entry
Database: PDB / ID: 5wxk
TitleEarP bound with domain I of EF-P
Components
  • EarP
  • Elongation factor P
KeywordsTRANSFERASE / glycosyltransferase / GT-B / EF-P / rhamnosylation / translation elongation / dTDP-rhamnose
Function / homology
Function and homology information


protein-arginine rhamnosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / translation elongation factor activity / cytoplasm
Similarity search - Function
Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / 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 ...Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / 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 / SH3 type barrels. / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / NICKEL (II) ION / THYMIDINE-5'-DIPHOSPHATE / Protein-arginine rhamnosyltransferase / Elongation factor P
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B / serotype 15
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EarP
B: Elongation factor P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26213
Polymers51,9982
Non-polymers1,26411
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-86 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.204, 57.254, 72.831
Angle α, β, γ (deg.)90.00, 101.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-783-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein EarP


Mass: 44219.992 Da / Num. of mol.: 1
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 / Production host: Escherichia coli (E. coli) / References: UniProt: E6MVV9
#2: Protein Elongation factor P / / EF-P


Mass: 7777.938 Da / Num. of mol.: 1 / Fragment: UNP residues 1-63
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: efp, NMH_0798 / Production host: Escherichia coli (E. coli) / References: UniProt: E6MVW0

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Non-polymers , 6 types, 488 molecules

#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes-NaOH buffer (pH 7.0) and 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→43.66 Å / Num. obs: 45727 / % possible obs: 99.8 % / Redundancy: 4.1 % / Net I/σ(I): 12.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.716 / % possible all: 98.3

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Processing

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

Resolution: 1.801→41.965 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.34
RfactorNum. reflection% reflection
Rfree0.2018 2282 4.99 %
Rwork0.157 --
obs0.1592 45715 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→41.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 70 477 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073783
X-RAY DIFFRACTIONf_angle_d0.9015152
X-RAY DIFFRACTIONf_dihedral_angle_d17.9412223
X-RAY DIFFRACTIONf_chiral_restr0.053539
X-RAY DIFFRACTIONf_plane_restr0.005660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8007-1.83990.29391320.25022655X-RAY DIFFRACTION98
1.8399-1.88270.28851520.2222703X-RAY DIFFRACTION100
1.8827-1.92980.23491500.20742715X-RAY DIFFRACTION100
1.9298-1.98190.24521210.18882710X-RAY DIFFRACTION100
1.9819-2.04030.22721410.18582713X-RAY DIFFRACTION100
2.0403-2.10610.22291440.17042709X-RAY DIFFRACTION100
2.1061-2.18140.20181420.16492674X-RAY DIFFRACTION100
2.1814-2.26870.19841410.15912700X-RAY DIFFRACTION100
2.2687-2.3720.20871450.15562715X-RAY DIFFRACTION100
2.372-2.4970.22191420.15382741X-RAY DIFFRACTION100
2.497-2.65340.21891590.15062671X-RAY DIFFRACTION100
2.6534-2.85830.2091260.15222727X-RAY DIFFRACTION100
2.8583-3.14580.21431450.15552722X-RAY DIFFRACTION100
3.1458-3.60080.17651500.13662732X-RAY DIFFRACTION100
3.6008-4.53580.16641370.1242759X-RAY DIFFRACTION100
4.5358-41.97640.16761550.15152787X-RAY DIFFRACTION99
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)
11.35260.3857-0.44061.466-0.11270.8089-0.1510.1482-0.32640.02120.00630.02620.24120.00660.12220.2035-0.00570.09560.1292-0.02960.248813.4564-15.277512.2057
21.3584-0.3761-0.18593.6701-0.44780.1406-0.18680.4896-0.5872-0.427-0.15350.22010.2687-0.24420.17570.2904-0.0460.10070.1902-0.10730.33351.5311-15.81411.0781
32.060.2462-0.84430.8836-0.18770.9523-0.0882-0.0907-0.29020.0449-0.04570.00480.11170.00940.10630.14680.0090.04710.09010.00020.164711.0945-6.332120.8562
43.64111.40850.54562.96570.12961.08280.0663-0.03560.362-0.02750.02160.0853-0.21820.0615-0.08350.131-0.01450.0670.107-0.01810.127325.106315.4238.7496
54.0214-0.1495-0.04482.4606-0.53880.1280.07950.25570.1579-0.2398-0.0934-0.07310.1067-0.02040.02560.16210.00180.05510.12920.00790.117927.522910.99460.6004
61.37970.2228-1.24031.2382-0.32421.5298-0.0268-0.0516-0.0731-0.0572-0.0475-0.11260.00370.12370.07810.0924-0.00870.01730.09370.00280.118325.09834.371413.1635
71.83351.0275-0.53762.4343-0.43191.29340.2119-0.21320.33720.1054-0.06450.1069-0.26550.1124-0.11580.1885-0.02730.08830.1205-0.05320.200718.489718.415620.9723
83.34483.6329-1.14916.653-0.49961.60530.1024-0.4374-0.3170.3804-0.2066-0.20940.05370.28810.05720.12710.0316-0.00790.18480.02050.113619.0099-0.903830.3456
98.1349-0.3701-4.62136.54850.41716.67560.05320.11240.3848-0.18250.14510.3852-0.3236-0.5785-0.19140.16960.01960.00450.21350.05030.2193-16.75092.11317.9747
108.6756-1.0441-1.89082.6190.56345.3418-0.00760.2951-0.61050.144-0.02210.33870.5867-0.48760.20350.2235-0.09710.00420.3502-0.09210.2172-19.8373-9.441924.6311
116.5121.7792-3.6892.668-0.65573.02190.3348-0.06190.45230.1344-0.07210.1722-0.1508-0.0912-0.30190.13370.00020.00320.18480.00730.1593-8.91782.164122.0987
127.9513.9358-8.58591.9496-4.24589.27310.3348-0.1870.25650.2501-0.12110.1081-0.36250.2146-0.20010.1402-0.0170.03440.1737-0.02790.1839-12.33-2.362827.9203
134.64962.0966-3.61275.2329-2.19987.32870.18170.53890.19970.11810.06160.6976-0.1964-0.6761-0.19730.1628-0.012-0.01330.19840.0260.2083-18.7304-2.176718.9166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 202 )
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 235 )
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 290 )
7X-RAY DIFFRACTION7chain 'A' and (resid 291 through 346 )
8X-RAY DIFFRACTION8chain 'A' and (resid 347 through 378 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 11 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 17 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 55 )
13X-RAY DIFFRACTION13chain 'B' and (resid 56 through 66 )

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