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- PDB-7z6a: CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL A... -

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Basic information

Entry
Database: PDB / ID: 7z6a
TitleCRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE
Components
  • 2'F-RNA (5'-D(*(GF2)P*(GF2)P*(CFZ)P*(CFZ)P*(AF2)P*(CFZ)P*(CFZ))-R(P*(A9Z))-3')
  • UDP-MurNAc-pentapeptide
  • UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
KeywordsTRANSFERASE / FEMX / Xeno-nucleic acids / PEPTIDOGLYCAN / PEPTIDYL-XNA CONJUGATE / TRANSFERASE-PEPTIDE-XNA COMPLEX
Function / homology
Function and homology information


UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase / UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
FemABX peptidyl transferase / : / FemAB family / FemABX peptidyl transferase family profile. / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
N-acetyl-alpha-muramic acid / URIDINE-5'-DIPHOSPHATE / DNA / UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
Similarity search - Component
Biological speciesWeissella viridescens (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLi de la Sierra-Gallay, I.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis.
Authors: Rietmeyer, L. / Li De La Sierra-Gallay, I. / Schepers, G. / Dorchene, D. / Iannazzo, L. / Patin, D. / Touze, T. / van Tilbeurgh, H. / Herdewijn, P. / Etheve-Quelquejeu, M. / Fonvielle, M.
History
DepositionMar 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
C: UDP-MurNAc-pentapeptide
B: 2'F-RNA (5'-D(*(GF2)P*(GF2)P*(CFZ)P*(CFZ)P*(AF2)P*(CFZ)P*(CFZ))-R(P*(A9Z))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0846
Polymers42,2943
Non-polymers7903
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.900, 100.880, 44.290
Angle α, β, γ (deg.)90.000, 110.650, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein / Protein/peptide / DNA chain / Sugars , 4 types, 4 molecules ACB

#1: Protein UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase


Mass: 39212.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella viridescens (bacteria) / Gene: femX / Production host: Escherichia coli (E. coli)
References: UniProt: Q9EY50, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase
#2: Protein/peptide UDP-MurNAc-pentapeptide


Mass: 463.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 2'F-RNA (5'-D(*(GF2)P*(GF2)P*(CFZ)P*(CFZ)P*(AF2)P*(CFZ)P*(CFZ))-R(P*(A9Z))-3')


Mass: 2617.633 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 8-nt peptidyl-oligonucleotide bi-substrate analog with 2-deoxy-2-fluoro ribonucleic acids, Residues GF2 B 2 and GFZ B 5 are linked by a polyethylene glycol not observed in the crystal structure
Source: (synth.) synthetic construct (others)
#6: Sugar ChemComp-MUB / N-acetyl-alpha-muramic acid / N-acetyl-muramic acid / N-ACETYLMURAMIC ACID


Type: D-saccharide, alpha linking / Mass: 293.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 136 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6 / Details: Tri-Na citrate , ammonium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980131 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980131 Å / Relative weight: 1
ReflectionResolution: 1.66→41.44 Å / Num. obs: 40415 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.62 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.23 / Net I/σ(I): 8.93
Reflection shellResolution: 1.66→1.76 Å / Num. unique obs: 6276 / CC1/2: 0.68 / Rrim(I) all: 1.49

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4II9

4ii9


Resolution: 1.66→41.44 Å / SU ML: 0.2407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 2018 5 %
Rwork0.1981 38323 -
obs0.1997 40341 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.79 Å2
Refinement stepCycle: LAST / Resolution: 1.66→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 177 6 134 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933013
X-RAY DIFFRACTIONf_angle_d1.26034124
X-RAY DIFFRACTIONf_chiral_restr0.0698451
X-RAY DIFFRACTIONf_plane_restr0.007519
X-RAY DIFFRACTIONf_dihedral_angle_d17.66751137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.3791360.36162567X-RAY DIFFRACTION92.32
1.7-1.750.35831430.29622733X-RAY DIFFRACTION99.93
1.75-1.80.29071430.2832704X-RAY DIFFRACTION99.82
1.8-1.860.28771440.25692760X-RAY DIFFRACTION99.9
1.86-1.920.31251450.24592743X-RAY DIFFRACTION99.62
1.92-20.29941440.22122745X-RAY DIFFRACTION99.86
2-2.090.2251450.20412753X-RAY DIFFRACTION99.86
2.09-2.20.2551470.19712778X-RAY DIFFRACTION99.86
2.2-2.340.23081440.20222732X-RAY DIFFRACTION99.86
2.34-2.520.26521420.20312713X-RAY DIFFRACTION99.86
2.52-2.770.27691460.21022763X-RAY DIFFRACTION99.9
2.77-3.170.23531450.20362763X-RAY DIFFRACTION99.93
3.18-40.20071460.16952762X-RAY DIFFRACTION100
4-41.440.14971480.1582807X-RAY DIFFRACTION99.93

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