[English] 日本語
Yorodumi
- PDB-1aok: VIPOXIN COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aok
TitleVIPOXIN COMPLEX
Components(VIPOXIN COMPLEX) x 2
KeywordsHYDROLASE / PHOSPHOLIPASE / VIPOXIN / PLA2-ACTIVITY / SNAKE-VENOM
Function / homology
Function and homology information


phospholipase A2 / calcium-independent phospholipase A2 activity / calcium-dependent phospholipase A2 activity / arachidonate secretion / negative regulation of T cell proliferation / lipid catabolic process / phospholipid metabolic process / phospholipid binding / toxin activity / killing of cells of another organism ...phospholipase A2 / calcium-independent phospholipase A2 activity / calcium-dependent phospholipase A2 activity / arachidonate secretion / negative regulation of T cell proliferation / lipid catabolic process / phospholipid metabolic process / phospholipid binding / toxin activity / killing of cells of another organism / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Acidic phospholipase A2 homolog vipoxin A chain / Basic phospholipase A2 vipoxin B chain
Similarity search - Component
Biological speciesVipera ammodytes meridionalis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPerbandt, M. / Wilson, J.C. / Eschenburg, S. / Betzel, C.
CitationJournal: FEBS Lett. / Year: 1997
Title: Crystal structure of vipoxin at 2.0 A: an example of regulation of a toxic function generated by molecular evolution.
Authors: Perbandt, M. / Wilson, J.C. / Eschenburg, S. / Mancheva, I. / Aleksiev, B. / Genov, N. / Willingmann, P. / Weber, W. / Singh, T.P. / Betzel, C.
History
DepositionJul 7, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VIPOXIN COMPLEX
B: VIPOXIN COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5563
Polymers27,4972
Non-polymers591
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 67.690, 46.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein VIPOXIN COMPLEX / PHOSPHOLIPASE A2 INHIBITOR AND PHOSPHOLIPASE A2


Mass: 13661.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: VENOM / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P04084, phospholipase A2
#2: Protein VIPOXIN COMPLEX / PHOSPHOLIPASE A2 INHIBITOR AND PHOSPHOLIPASE A2


Mass: 13835.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: VENOM / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P14420, phospholipase A2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN VIPOXIN ONE SUBUNIT IS ROTATED BY ABOUT 180 DEGREE TO GIVE A PSEUDO MIRROR SYMMETRY AND THE ...IN VIPOXIN ONE SUBUNIT IS ROTATED BY ABOUT 180 DEGREE TO GIVE A PSEUDO MIRROR SYMMETRY AND THE COMPLEX IS STABILIZED BY TWELVE INTERMOLECULAR CONTACTS WHICH OBVIOUSLY DIFFER FROM OTHER DIMERIC PHOSPHOLIPASES A2.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 36.88 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
214 %PEG33501reservoir
315 %PEG4001reservoir
410 mM1reservoirCaCl2
5100 mMNa acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1995 / Details: COLLIMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15070 / % possible obs: 100 % / Observed criterion σ(I): 2 / Rsym value: 0.086
Reflection shellResolution: 2→2.03 Å / Rsym value: 0.274 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.274

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 2→20 Å /
Rfactor% reflection
Rfree0.23 5 %
Rwork0.16 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 4 291 2204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.025
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16
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://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