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- PDB-6mvz: Mle-Phe-Mle-Phe. Linear precursor of pseudoxylallemycin A. -

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Basic information

Entry
Database: PDB / ID: 6mvz
TitleMle-Phe-Mle-Phe. Linear precursor of pseudoxylallemycin A.
ComponentsLinear precursor of pseudoxylallemycin A
KeywordsANTIBIOTIC / tetrapeptide / N-methyl leucine / linear precursor of pseudoxylallemycin A
Function / homologyLinear precursor of pseudoxylallemycin A / trifluoroacetic acid
Function and homology information
Biological speciesXylaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.83 Å
AuthorsCameron, A.J. / Harris, P.W.R. / Brimble, M.A. / Squire, C.J.
CitationJournal: Org.Biomol.Chem. / Year: 2019
Title: Investigations of the key macrolactamisation step in the synthesis of cyclic tetrapeptide pseudoxylallemycin A.
Authors: Cameron, A.J. / Squire, C.J. / Gerenton, A. / Stubbing, L.A. / Harris, P.W.R. / Brimble, M.A.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Linear precursor of pseudoxylallemycin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6812
Polymers5671
Non-polymers1141
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)8.255, 19.173, 23.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Linear precursor of pseudoxylallemycin A


Type: Peptide-like / Class: Antibiotic / Mass: 566.730 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Mle-Phe-Mle-Phe. Linear precursor of pseudoxylallemycin A. The peptide is linear, unlike Mle-Phe-Mle-Phe Pseudoxylallemycin A that is cyclic.
Source: (synth.) Xylaria (fungus) / References: Linear precursor of pseudoxylallemycin A
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 1.64 Å3/Da / Density % sol: 24.86 %
Crystal growTemperature: 293 K / Method: evaporation / Details: ethanol, water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.71075 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71075 Å / Relative weight: 1
ReflectionResolution: 0.83→23.44 Å / Num. obs: 4332 / % possible obs: 98 % / Redundancy: 14.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Net I/σ(I): 22.9
Reflection shellResolution: 0.83→0.85 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 16.5 / Num. unique obs: 253 / CC1/2: 0.99 / Rpim(I) all: 0.038 / % possible all: 83.8

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata reduction
Aimlessdata scaling
SHELXSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.83→23.44 Å / Cross valid method: NONE
Details: full least squares refinement using SHELXL, anisotropic atoms, riding hydrogens.
RfactorNum. reflection% reflection
obs0.0675 4332 100 %
Refinement stepCycle: LAST / Resolution: 0.83→23.44 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms41 0 7 1 49

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