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- PDB-6oyz: Crystal structure of MraY bound to capuramycin -

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Basic information

Entry
Database: PDB / ID: 6oyz
TitleCrystal structure of MraY bound to capuramycin
Components
  • MraYAA nanobody
  • Phospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsMEMBRANE PROTEIN/TRANSFERASE / peptidoglycan biosynthesis / antibiotic target / integral membrane enzyme / translocase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate 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 division / metal ion binding ...phospho-N-acetylmuramoyl-pentapeptide-transferase / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate 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 division / metal ion binding / identical protein 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-NKM / Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesLama glama (llama)
Aquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 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: 2019
Title: Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Authors: Mashalidis, E.H. / Kaeser, B. / Terasawa, Y. / Katsuyama, A. / Kwon, D.Y. / Lee, K. / Hong, J. / Ichikawa, S. / Lee, S.Y.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)224,6199
Polymers224,0498
Non-polymers5701
Water00
1
E: MraYAA nanobody
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5823
Polymers56,0122
Non-polymers5701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: MraYAA nanobody
C: 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
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)93.759, 128.067, 129.516
Angle α, β, γ (deg.)90.00, 110.82, 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 (strain VF5) (bacteria)
Strain: VF5 / Gene: mraY, aq_053 / Variant: VF5 / Production host: Escherichia coli (E. coli)
References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase
#3: Chemical ChemComp-NKM / (2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide


Mass: 569.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N5O12
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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 18% polyethylene glycol 4000, 0.4 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: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.62→87.64 Å / Num. obs: 32765 / % possible obs: 99.95 % / Redundancy: 15.2 % / CC1/2: 0.989 / Net I/σ(I): 10.25
Reflection shellResolution: 3.62→3.749 Å / Num. unique obs: 3244 / CC1/2: 0.343

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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: 5CKR

5ckr


Resolution: 3.62→87.637 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.2
RfactorNum. reflection% reflection
Rfree0.3008 1420 4.34 %
Rwork0.2767 --
obs0.2777 32752 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.62→87.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12904 0 40 0 12944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513254
X-RAY DIFFRACTIONf_angle_d0.7518125
X-RAY DIFFRACTIONf_dihedral_angle_d10.3984259
X-RAY DIFFRACTIONf_chiral_restr0.0492198
X-RAY DIFFRACTIONf_plane_restr0.0042219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6201-3.74950.3951370.37293101X-RAY DIFFRACTION100
3.7495-3.89960.32011350.31683144X-RAY DIFFRACTION100
3.8996-4.07710.36981470.29343108X-RAY DIFFRACTION100
4.0771-4.2920.31491420.26423096X-RAY DIFFRACTION100
4.292-4.56090.25661400.23823140X-RAY DIFFRACTION100
4.5609-4.91310.26731440.22363133X-RAY DIFFRACTION100
4.9131-5.40740.31051430.25463122X-RAY DIFFRACTION100
5.4074-6.18970.31891370.28383144X-RAY DIFFRACTION100
6.1897-7.79760.28261470.28893142X-RAY DIFFRACTION100
7.7976-87.66230.29091480.28773202X-RAY DIFFRACTION100

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