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- PDB-4ii9: Crystal structure of Weissella viridescens FemXVv non-ribosomal a... -

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Basic information

Entry
Database: PDB / ID: 4ii9
TitleCrystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate
Components
  • 5-mer peptide
  • FemX
  • RNA (5'-R(P*CP*CP*(A9Z))-3')
KeywordsTRANSFERASE/PEPTIDE/RNA / FEMX / PEPTIDOGLYCAN / transferase / peptidyl-RNA conjugate complex / TRANSFERASE-PEPTIDE-RNA 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. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-muramic acid / URIDINE-5'-DIPHOSPHATE / RNA / UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
Similarity search - Component
Biological speciesWeissella viridescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLi de la Sierra-Gallay, I. / Fonvielle, M. / van Tilbeurgh, H. / Arthur, M. / Etheve-Quelquejeu, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors
Authors: Fonvielle, M. / Li de La Sierra-Gallay, I. / El-Sagheer, A.H. / Lecerf, M. / Patin, D. / Mellal, D. / Mayer, C. / Blanot, D. / Gale, N. / Brown, T. / van Tilbeurgh, H. / Etheve-Quelquejeu, M. / Arthur, M.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FemX
B: 5-mer peptide
C: RNA (5'-R(P*CP*CP*(A9Z))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4406
Polymers40,6503
Non-polymers7903
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-16 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.130, 101.770, 46.320
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

#1: Protein FemX


Mass: 39212.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella viridescens (bacteria) / Strain: CIP102810T / Gene: femX / Plasmid: pTrc-His60 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q9EY50, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase
#2: Protein/peptide 5-mer peptide


Mass: 463.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: RNA chain RNA (5'-R(P*CP*CP*(A9Z))-3')


Mass: 973.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#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: obtained synthetically / Formula: C11H19NO8
IdentifierTypeProgram
a-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 298 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 / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Tris-sodium citrate buffer, 0.2M ammonium acetate, 33% polyethylene glycol 4k, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012 / Details: mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.66→38.12 Å / Num. all: 44718 / Num. obs: 44718 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.8
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.9 / Num. unique all: 7126 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MXCubedata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GKR

3gkr


Resolution: 1.66→38.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.632 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20935 2236 5 %RANDOM
Rwork0.17487 ---
all0.178 44718 --
obs0.17661 42482 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20.41 Å2
2---1.07 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.66→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 68 49 296 3140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192924
X-RAY DIFFRACTIONr_angle_refined_deg2.3421.9873978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09924.388139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13515466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7421517
X-RAY DIFFRACTIONr_chiral_restr0.170.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212209
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 158 -
Rwork0.27 3011 -
obs--96.53 %

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