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- PDB-7z5y: CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL A... -

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Basic information

Entry
Database: PDB / ID: 7z5y
TitleCRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE
Components
  • HNA (5'-D(P*(6HA)P*(6HC)P*(6HC))-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: 1.71 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 10, 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: Atomic model / Data collection ...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 / 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_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_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
B: HNA (5'-D(P*(6HA)P*(6HC)P*(6HC))-R(P*(A9Z))-3')
C: UDP-MurNAc-pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7636
Polymers40,9733
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)42.160, 101.960, 46.190
Angle α, β, γ (deg.)90.000, 102.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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

#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: DNA chain HNA (5'-D(P*(6HA)P*(6HC)P*(6HC))-R(P*(A9Z))-3')


Mass: 1297.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide UDP-MurNAc-pentapeptide


Mass: 463.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: Tri-sodium citrate , ammonium acetate, PEG 4000 / PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.71→41.2 Å / Num. obs: 38530 / % possible obs: 94 % / Redundancy: 6 % / Biso Wilson estimate: 27.38 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.267 / Net I/σ(I): 5.22
Reflection shellResolution: 1.71→1.82 Å / Mean I/σ(I) obs: 0.77 / Num. unique obs: 4605 / CC1/2: 0.31 / Rrim(I) all: 2.925 / % possible all: 69.9

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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: 1.71→41.2 Å / SU ML: 0.2665 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1894 5.01 %RANDOM
Rwork0.2119 35939 --
obs0.2134 37833 92.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.35 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 91 6 134 2996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822928
X-RAY DIFFRACTIONf_angle_d1.00173978
X-RAY DIFFRACTIONf_chiral_restr0.0572433
X-RAY DIFFRACTIONf_plane_restr0.0063519
X-RAY DIFFRACTIONf_dihedral_angle_d9.6727446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.790.43521500.42312791X-RAY DIFFRACTION58.26
1.79-1.890.3942180.37944191X-RAY DIFFRACTION86.71
1.89-2.010.38172520.32314764X-RAY DIFFRACTION98.3
2.01-2.160.33282520.26374802X-RAY DIFFRACTION99.9
2.16-2.380.2632550.21084841X-RAY DIFFRACTION99.98
2.38-2.720.23112540.21194819X-RAY DIFFRACTION99.84
2.72-3.430.22462550.19574846X-RAY DIFFRACTION99.96
3.43-41.20.18212580.16674885X-RAY DIFFRACTION99.59

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