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- PDB-2mlt: MELITTIN -

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Basic information

Entry
Database: PDB / ID: 2mlt
TitleMELITTIN
ComponentsMELITTIN
KeywordsTOXIN (HEMOLYTIC POLYPEPTIDE)
Function / homology
Function and homology information


other organism cell membrane / molecular function inhibitor activity / porin activity / pore complex / protein kinase inhibitor activity / 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
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEisenberg, D. / Gribskov, M. / Terwilliger, T.C.
Citation
#1: Journal: J.Biol.Chem. / Year: 1982
Title: The Structure of Melittin. I. Structure Determination and Partial Refinement.
Authors: Terwilliger, T.C. / Eisenberg, D.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: The Structure of Melittin. II. Interpretation of the Structure
Authors: Terwilliger, T.C. / Eisenberg, D.
#3: Journal: J.Biol.Chem. / Year: 1980
Title: Melittin Forms Crystals which are Suitable for High Resolution X-Ray Structural Analysis and which Reveal a Molecular 2-Fold Axis of Symmetry
Authors: Anderson, D. / Terwilliger, T.C. / Wickner, W. / Eisenberg, D.
History
DepositionOct 4, 1990Processing site: BNL
SupersessionOct 15, 1990ID: 1MLT
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MELITTIN
B: MELITTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8934
Polymers5,7012
Non-polymers1922
Water41423
1
A: MELITTIN
B: MELITTIN
hetero molecules

A: MELITTIN
B: MELITTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7868
Polymers11,4024
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5220 Å2
ΔGint-84 kcal/mol
Surface area6280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.832, 38.293, 42.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-36-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99631, -0.03387, -0.07887), (0.04805, -0.98147, -0.18547), (-0.07113, -0.18858, 0.97948)
Vector: 71.251, 2.711, 2.053)

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Components

#1: Protein/peptide MELITTIN


Mass: 2850.495 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / References: UniProt: P01501
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Anderson, D., (1980) J.Biol.Chem., 255, 2578.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-20 mg/ml1drop
25 M1dropNaHCO2
35 Msatammonium sulfate1droppH7.2
40.02 Msodium phosphate1droppH7.2
55 M1reservoirNaHCO2
60.02 Msodium phosphate1reservoirpH7.2

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.4 Å / Num. obs: 2705 / Num. measured all: 5758 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→20 Å /
RfactorNum. reflection
obs0.198 137
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms402 0 10 23 435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0460.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0730.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.0791.5
X-RAY DIFFRACTIONp_mcangle_it2.9132
X-RAY DIFFRACTIONp_scbond_it4.0432
X-RAY DIFFRACTIONp_scangle_it6.2813
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.5
X-RAY DIFFRACTIONp_multtor_nbd0.2090.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.5440.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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