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- PDB-6rtg: Crystal structure of the UDP-bound glycosyltransferase domain fro... -

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Basic information

Entry
Database: PDB / ID: 6rtg
TitleCrystal structure of the UDP-bound glycosyltransferase domain from the YGT toxin
ComponentsRTX toxin and Ca2+-binding protein
KeywordsTOXIN / Glycosyltransferase domain / Nucleotide binding
Function / homology
Function and homology information


glycosyltransferase activity / :
Similarity search - Function
TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / : / URIDINE-5'-DIPHOSPHATE / RTX toxin and Ca2+-binding protein
Similarity search - Component
Biological speciesYersinia mollaretii
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWirth, C. / Bogdanovic, X. / Kao, W.-C. / Hunte, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCRC 746 Germany
German Federal Ministry for Education and ResearchEXC-2189 Germany
CitationJournal: Sci Adv / Year: 2020
Title: Inverse control of Rab proteins byYersiniaADP-ribosyltransferase and glycosyltransferase related to clostridial glucosylating toxins.
Authors: Ost, G.S. / Wirth, C. / Bogdanovic, X. / Kao, W.C. / Schorch, B. / Aktories, P.J.K. / Papatheodorou, P. / Schwan, C. / Schlosser, A. / Jank, T. / Hunte, C. / Aktories, K.
History
DepositionMay 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RTX toxin and Ca2+-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,64912
Polymers59,6541
Non-polymers99511
Water7,350408
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint7 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.270, 164.270, 47.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1108-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RTX toxin and Ca2+-binding protein


Mass: 59653.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia mollaretii (strain ATCC 43969 / DSM 18520 / CIP 103324 / CNY 7263 / WAIP 204) (bacteria)
Strain: ATCC 43969 / DSM 18520 / CIP 103324 / CNY 7263 / WAIP 204
Gene: ymoll0001_37990 / Production host: Escherichia coli (E. coli) / References: UniProt: C4SH25

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: Long rods
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM sodium acetate and 15 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52064 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.184 / Net I/σ(I): 12.07
Reflection shellResolution: 1.9→2 Å / Redundancy: 19.2 % / Rmerge(I) obs: 2.083 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7314 / CC1/2: 0.525 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
autoSHARPphasing
PHENIXphasing
XSCALEdata scaling
XDSdata reduction
MxCuBEdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.56 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.41
RfactorNum. reflection% reflection
Rfree0.2225 2082 4 %
Rwork0.1856 --
obs0.187 52064 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 59 408 4535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054298
X-RAY DIFFRACTIONf_angle_d0.645827
X-RAY DIFFRACTIONf_dihedral_angle_d12.6372592
X-RAY DIFFRACTIONf_chiral_restr0.044653
X-RAY DIFFRACTIONf_plane_restr0.004748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94430.32041360.29293271X-RAY DIFFRACTION100
1.9443-1.99290.32381380.27163299X-RAY DIFFRACTION100
1.9929-2.04680.30851350.26183247X-RAY DIFFRACTION100
2.0468-2.1070.27641370.24093285X-RAY DIFFRACTION100
2.107-2.1750.26841370.22593298X-RAY DIFFRACTION100
2.175-2.25280.27821370.21073277X-RAY DIFFRACTION100
2.2528-2.3430.21371380.20083310X-RAY DIFFRACTION100
2.343-2.44960.22731370.19663297X-RAY DIFFRACTION100
2.4496-2.57870.25361370.19873298X-RAY DIFFRACTION100
2.5787-2.74030.26591390.19423323X-RAY DIFFRACTION100
2.7403-2.95180.20631390.19053343X-RAY DIFFRACTION100
2.9518-3.24880.22341390.18513341X-RAY DIFFRACTION100
3.2488-3.71870.20611420.16983385X-RAY DIFFRACTION100
3.7187-4.68440.17831420.14823409X-RAY DIFFRACTION100
4.6844-45.57340.20761490.1733599X-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)
14.3326-0.97470.44492.84780.58841.8659-0.7369-0.91660.94140.87170.607-0.1116-0.05520.08040.09230.39180.183-0.23580.41-0.26690.365186.8126128.923334.3501
23.8538-1.8515-0.24412.59290.10560.8489-0.18730.0425-0.24820.14330.09240.26390.0772-0.07690.06710.22070.01360.02460.2144-0.03640.169780.5941116.77721.9729
38.1591-2.32350.62960.7374-0.00781.13560.26950.7458-1.1104-0.1643-0.29850.90610.2376-0.08930.01260.29710.0044-0.06160.3674-0.12570.551875.5891110.204315.2554
42.40681.2772-0.51444.9323-0.98432.41850.12050.53141.2689-0.7403-0.0898-1.6927-0.22050.69650.02250.3380.00020.1620.50880.15191.0883107.5751123.332116.7966
56.7374-0.75732.35494.3923-2.51954.6353-0.39171.11840.6056-1.0748-0.287-0.85380.50060.2840.49670.44220.0180.1520.38560.18980.8346100.7656128.25114.585
64.1785-1.8036-0.07911.94440.08390.94190.20520.60550.2621-0.2887-0.3178-0.19420.09250.07150.1110.28440.06150.00120.34640.04790.168689.3001119.157213.1158
71.55880.565-0.98624.8844-0.41171.5006-0.24970.38681.4797-0.24870.0424-0.1761-0.3853-0.11160.18520.42250.0545-0.17040.37250.10690.820673.7632146.356515.6296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 316 )
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 357 )
5X-RAY DIFFRACTION5chain 'A' and (resid 358 through 384 )
6X-RAY DIFFRACTION6chain 'A' and (resid 385 through 438 )
7X-RAY DIFFRACTION7chain 'A' and (resid 439 through 518 )

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