[English] 日本語
Yorodumi
- PDB-2mlt: MELITTIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mlt
TitleMELITTIN
ComponentsMELITTIN
KeywordsTOXIN (HEMOLYTIC POLYPEPTIDE)
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more