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- PDB-8cxr: Crystal structure of MraY bound to a sphaerimicin analogue -

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Basic information

Entry
Database: PDB / ID: 8cxr
TitleCrystal structure of MraY bound to a sphaerimicin analogue
Components
  • MraYAA nanobody
  • Phospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsMEMBRANE PROTEIN/Transferase / MraY / nanobody / sphaerimicin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Transferase complex
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division ...phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Chem-P5L / Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesLama glama (llama)
Aquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsMashalidis, E.H. / Lee, S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY.
Authors: Nakaya, T. / Yabe, M. / Mashalidis, E.H. / Sato, T. / Yamamoto, K. / Hikiji, Y. / Katsuyama, A. / Shinohara, M. / Minato, Y. / Takahashi, S. / Horiuchi, M. / Yokota, S.I. / Lee, S.Y. / Ichikawa, S.
History
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: MraYAA nanobody
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
G: MraYAA nanobody
C: Phospho-N-acetylmuramoyl-pentapeptide-transferase
F: MraYAA nanobody
B: Phospho-N-acetylmuramoyl-pentapeptide-transferase
H: MraYAA nanobody
D: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,61910
Polymers224,0498
Non-polymers1,5702
Water00
1
E: MraYAA nanobody
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7973
Polymers56,0122
Non-polymers7851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: MraYAA nanobody
C: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7973
Polymers56,0122
Non-polymers7851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: MraYAA nanobody
B: Phospho-N-acetylmuramoyl-pentapeptide-transferase


Theoretical massNumber of molelcules
Total (without water)56,0122
Polymers56,0122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: MraYAA nanobody
D: Phospho-N-acetylmuramoyl-pentapeptide-transferase


Theoretical massNumber of molelcules
Total (without water)56,0122
Polymers56,0122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.884, 127.704, 130.150
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
MraYAA nanobody


Mass: 15057.651 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein
Phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-MurNAc-pentapeptide phosphotransferase


Mass: 40954.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: mraY, aq_053 / Production host: Escherichia coli (E. coli)
References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase
#3: Chemical ChemComp-P5L / (1S,4R,5S,6R,7S,9S,10S,11S,13S,14R)-9-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]-14-(hexadecanoyloxy)-5,6,13-trihydroxy-8,16-dioxa-2,11-diazatricyclo[9.3.1.1~4,7~]hexadecane-10-carboxylic acid / sphaerimicin analogue


Mass: 784.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H60N4O14 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 18% polyethylene glycol 4000, 0.2 M ammonium thiocyanate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.65→87.905 Å / Num. obs: 31954 / % possible obs: 99.45 % / Redundancy: 6.6 % / CC1/2: 0.994 / Net I/σ(I): 8.19
Reflection shellResolution: 3.65→3.78 Å / Num. unique obs: 3174 / CC1/2: 0.346

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OYZ

6oyz


Resolution: 3.65→87.905 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2946 1378 4.33 %
Rwork0.249 --
obs0.251 31792 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.65→87.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13254 0 110 0 13364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213689
X-RAY DIFFRACTIONf_angle_d0.52518687
X-RAY DIFFRACTIONf_dihedral_angle_d9.2737811
X-RAY DIFFRACTIONf_chiral_restr0.0412257
X-RAY DIFFRACTIONf_plane_restr0.0042271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.78050.42551290.34623024X-RAY DIFFRACTION99
3.7805-3.93190.34291420.30372953X-RAY DIFFRACTION98
3.9319-4.11080.33011290.25613017X-RAY DIFFRACTION99
4.1108-4.32750.28681470.20283048X-RAY DIFFRACTION100
4.3275-4.59870.23871350.1913000X-RAY DIFFRACTION100
4.5987-4.95370.22531350.18723086X-RAY DIFFRACTION100
4.9537-5.45210.29421410.20823026X-RAY DIFFRACTION100
5.4521-6.24090.32771350.24243071X-RAY DIFFRACTION100
6.2409-7.86210.29951410.27043068X-RAY DIFFRACTION100
7.8621-87.9050.29591440.28323121X-RAY DIFFRACTION100

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