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- PDB-6o4m: Racemic melittin -

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Basic information

Entry
Database: PDB / ID: 6o4m
TitleRacemic melittin
Components
  • D-Melittin
  • Melittin
KeywordsTOXIN / racemic / cytotoxic / antimicrobial
Function / homology
Function and homology information


other organism cell membrane / porin activity / molecular function inhibitor activity / protein kinase inhibitor activity / pore complex / localization / monoatomic ion transport / toxin activity / killing of cells of another organism / lipid binding / extracellular region
Similarity search - Function
Melittin/ Api allergen / Melittin
Similarity search - Domain/homology
polypeptide(D) / polypeptide(D) (> 10) / Melittin
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsKurgan, K.W. / Bingman, C.A. / Gellman, S.H. / Forest, K.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM061238 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Retention of Native Quaternary Structure in Racemic Melittin Crystals.
Authors: Kurgan, K.W. / Kleman, A.F. / Bingman, C.A. / Kreitler, D.F. / Weisblum, B. / Forest, K.T. / Gellman, S.H.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: D-Melittin
A: Melittin
B: Melittin
C: D-Melittin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,26113
Polymers11,3964
Non-polymers8659
Water2,864159
1
D: D-Melittin
hetero molecules

D: D-Melittin
hetero molecules

C: D-Melittin
hetero molecules

C: D-Melittin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,15812
Polymers11,3904
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_647-x+3/2,y-1/2,-z+21
Buried area5850 Å2
ΔGint-128 kcal/mol
Surface area6620 Å2
MethodPISA
2
A: Melittin
B: Melittin
hetero molecules

A: Melittin
B: Melittin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,36314
Polymers11,4024
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6030 Å2
ΔGint-141 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.380, 58.990, 44.020
Angle α, β, γ (deg.)90.00, 110.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Polypeptide(D) D-Melittin / MLT / Allergen Api m 3 / Allergen Api m III


Mass: 2847.474 Da / Num. of mol.: 2 / Fragment: residues 44-69 / Source method: obtained synthetically / Source: (synth.) Apis mellifera (honey bee) / References: UniProt: P01501
#2: Protein/peptide Melittin / / MLT / Allergen Api m 3 / Allergen Api m III


Mass: 2850.495 Da / Num. of mol.: 2 / Fragment: residues 44-69 / Source method: obtained synthetically / Source: (synth.) Apis mellifera (honey bee) / References: UniProt: P01501
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD-form of Melittin is comprised of D-amino acids

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Description: A FEW ADDITIONAL MINOR CONFORMATIONS OF SIDE CHAINS AND SOLVENT MOLECULES WERE OBSERVED IN THE ELECTRON DENSITY MAP BUT OMITTED FROM THE MODEL.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M ammonium sulfate, 0.1 M BIS-TRIS pH = 6.5, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.68877 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68877 Å / Relative weight: 1
ReflectionResolution: 1.27→41.2 Å / Num. obs: 24139 / % possible obs: 99.4 % / Redundancy: 14 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Rsym value: 0.071 / Net I/σ(I): 10.8
Reflection shellResolution: 1.27→1.3 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2371 / CC1/2: 0.887 / Rrim(I) all: 1.153 / Rsym value: 1.069 / % possible all: 98.4

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MLT

2mlt


Resolution: 1.27→23.98 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2369 9.8 %Random selection
Rwork0.201 ---
obs-24108 99.45 %-
Displacement parametersBiso mean: 17.4 Å2
Refinement stepCycle: LAST / Resolution: 1.27→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 45 159 1008
LS refinement shellResolution: 1.27→1.2855 Å
RfactorNum. reflection% reflection
Rfree0.333 135 9 %
Rwork0.325 1505 -
obs--97.5 %

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