[English] 日本語
Yorodumi
- PDB-1joh: THE STRUCTURE OF ANTIAMOEBIN I, A MEMBRANE-ACTIVE PEPTIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1joh
TitleTHE STRUCTURE OF ANTIAMOEBIN I, A MEMBRANE-ACTIVE PEPTIDE
ComponentsANTIAMOEBIN I
KeywordsANTIBIOTIC / ANTIAMOEBIN I / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL
Function / homologyAntiamoebin 1 / METHANOL / :
Function and homology information
Biological speciesEMERICELLOPSIS (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSnook, C.F. / Wallace, B.A.
Citation
Journal: Structure / Year: 1998
Title: The Structure and Function of Antiamoebin I, a Proline-Rich Membrane-Active Polypeptide.
Authors: Snook, C.F. / Woolley, G.A. / Oliva, G. / Pattabhi, V. / Wood, S.F. / Blundell, T.L. / Wallace, B.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Molecular-Replacement Solution of an Intermediate-Sized Helical Polypeptide, Antiamoebin I.
Authors: Snook, C.F. / Wallace, B.A.
#2: Journal: Thesis, University of London / Year: 1997
Title: The Structure and Function of Antiamoebin I, a Membrane-Active Peptide
Authors: Snook, C.F.
#3: Journal: Thesis, University of London / Year: 1988
Title: Molecular Redundancy and Protein Crystallography : X-Ray Structure Analysis of Antiamoebin I, Bovine Pancreatic Polypeptide and Human Serum Amyloid P Component
Authors: Oliva, G.
History
DepositionOct 11, 1997Processing site: BNL
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Mar 4, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / refine / reflns / struct_conn
Item: _chem_comp.pdbx_synonyms / _pdbx_database_status.process_site ..._chem_comp.pdbx_synonyms / _pdbx_database_status.process_site / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIAMOEBIN I
B: ANTIAMOEBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,04725
Polymers3,3102
Non-polymers73723
Water00
1
A: ANTIAMOEBIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,00712
Polymers1,6551
Non-polymers35211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIAMOEBIN I
hetero molecules


  • defined by author
  • 2.04 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,03913
Polymers1,6551
Non-polymers38512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.530, 28.820, 9.060
Angle α, β, γ (deg.)88.90, 96.64, 123.85
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (-1) / Vector: 115.46)

-
Components

#1: Protein/peptide ANTIAMOEBIN I


Type: Peptaibol / Class: Antibiotic / Mass: 1654.991 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ANTIAMOEBIN I IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0)
Source: (natural) EMERICELLOPSIS (fungus) / References: NOR: NOR00945, Antiamoebin 1
#2: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH4O
Compound detailsANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...ANTIAMOEBIN I IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, ANTIAMOEBIN I IS REPRESENTED BY THE SEQUENCE (SEQRES)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28 % / Description: USED NORMALISED STRUCTURE FACTORS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 170 mg/ml / Common name: peptide

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: HILGER-WATTS / Detector: DIFFRACTOMETER / Date: 1986
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. obs: 6715 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.012 / Net I/σ(I): 10.5

-
Processing

Software
NameClassification
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RESIDUES 6 - 16 OF LEU1-ZERVAMICIN WITH ALL NON -EQUIVALENT SIDE-CHAINS TRIMMED TO ALA.

Resolution: 1.4→25 Å / Num. parameters: 1074 / Num. restraintsaints: 982 / σ(F): 0 / StereochEM target val spec case: HETATM DATA FROM CCSD / Stereochemistry target values: ENGH AND HUBER
Details: REFINEMENT STARTED USING 10.0 TO 2.5A AND DATA CUT-OFF AT 2 SIGMA IN X-PLOR. HIGH RESOLUTION LIMIT INCREASED TO 2.0A, LOW RESOLUTION DECREASED TO 25.0A AND DATA CUT-OFF DECREASED TO 0.0 ...Details: REFINEMENT STARTED USING 10.0 TO 2.5A AND DATA CUT-OFF AT 2 SIGMA IN X-PLOR. HIGH RESOLUTION LIMIT INCREASED TO 2.0A, LOW RESOLUTION DECREASED TO 25.0A AND DATA CUT-OFF DECREASED TO 0.0 SIGMA AT 2.0A RESOLUTION. RESOLUTION INCREASED FROM 2.0A TO 1.4A WITH ALL DATA USING SHELXL-93. REFINEMENT CEASED AFTER RESIDUES 1 TO 5 IN B-CHAIN IDENTIFIED AS DISORDERED IN DENSITY.
RfactorNum. reflection% reflection
all0.156 4359 -
obs0.156 4359 95.4 %
Refine analyzeOccupancy sum non hydrogen: 268
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 30 0 268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.036
X-RAY DIFFRACTIONs_angle_d3.152
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.065
Refinement
*PLUS
Rfactor all: 0.156
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