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- PDB-5ckr: Crystal Structure of MraY in complex with Muraymycin D2 -

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Basic information

Entry
Database: PDB / ID: 5ckr
TitleCrystal Structure of MraY in complex with Muraymycin D2
ComponentsPhospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsTRANSFERASE/ANTIBIOTIC / ALPHA-HELICAL / PNPT Superfamily / phospho-MurNAc-pentapeptide translocase / Membrane Protein / Bacterial cell wall / synthesis / natural product inhibitor / TRANSFERASE-ANTIBIOTIC 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
Muraymycin D2 / Phospho-N-acetylmuramoyl-pentapeptide-transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLee, S.Y. / Chung, B.C. / Mashalidis, E.H. / Tanino, T. / Kim, M. / Hong, J. / Ichikawa, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100984 United States
CitationJournal: Nature / Year: 2016
Title: Structural insights into inhibition of lipid I production in bacterial cell wall synthesis.
Authors: Chung, B.C. / Mashalidis, E.H. / Tanino, T. / Kim, M. / Matsuda, A. / Hong, J. / Ichikawa, S. / Lee, S.Y.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8712
Polymers40,9551
Non-polymers9161
Water1629
1
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules

A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7414
Polymers81,9092
Non-polymers1,8322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2700 Å2
ΔGint-26 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.480, 102.050, 135.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phospho-N-acetylmuramoyl-pentapeptide-transferase / / UDP-MurNAc-pentapeptide phosphotransferase


Mass: 40954.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: mraY, aq_053 / Plasmid: pET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C41
References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase
#2: Chemical ChemComp-57M / Muraymycin D2 / N-({(1S)-2-{[(2S)-1-{[3-({(1S,2S)-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxo -3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]ethyl}amino)propyl]amino}-4-methyl-1-oxopentan-2-yl]am ino}-1-[(4S)-2-amino-3,4,5,6-tetrahydropyrimidin-4-yl]-2-oxoethyl}carbamoyl)-L-valine


Mass: 915.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H61N11O16
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4 Å3/Da / Density % sol: 69.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 50 mM MgCl2, 40% PEG400, and 100 mM sodium cacodylate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→67.9 Å / Num. obs: 14178 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 4.6
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM0.6.1data reduction
Coot0.8-premodel building
iMOSFLM0.7.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J72

4j72


Resolution: 2.95→51.025 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 702 5 %
Rwork0.247 --
obs0.2477 14053 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→51.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 64 9 2638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082700
X-RAY DIFFRACTIONf_angle_d1.1393682
X-RAY DIFFRACTIONf_dihedral_angle_d12.763900
X-RAY DIFFRACTIONf_chiral_restr0.049448
X-RAY DIFFRACTIONf_plane_restr0.006432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.17780.38141340.35482562X-RAY DIFFRACTION97
3.1778-3.49750.32451690.29732620X-RAY DIFFRACTION100
3.4975-4.00340.24331320.23372660X-RAY DIFFRACTION100
4.0034-5.04310.20651290.20712708X-RAY DIFFRACTION100
5.0431-51.03260.25431380.24032801X-RAY DIFFRACTION100

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