[English] 日本語
Yorodumi
- PDB-1jlt: Vipoxin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jlt
TitleVipoxin Complex
Components
  • PHOSPHOLIPASE A2
  • PHOSPHOLIPASE A2 INHIBITOR
KeywordsHYDROLASE / HETERODIMER COMPLEX / PHOSPHOLIPASE / VIPOXIN / PLA2-ACTIVITY
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / 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
Acidic phospholipase A2 homolog vipoxin A chain / Basic phospholipase A2 vipoxin B chain
Similarity search - Component
Biological speciesVipera ammodytes ammodytes (western sand viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBanumathi, S. / Rajashankar, K.R. / Notzel, C. / Aleksiev, B. / Singh, T.P. / Genov, N. / Betzel, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the neurotoxic complex vipoxin at 1.4 A resolution.
Authors: Banumathi, S. / Rajashankar, K.R. / Notzel, C. / Aleksiev, B. / Singh, T.P. / Genov, N. / Betzel, C.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence The authors' residue numbering is not sequential. Residue numbers 15, 57, 60, 62-67, 87, ...sequence The authors' residue numbering is not sequential. Residue numbers 15, 57, 60, 62-67, 87, 123 are not used in the coordinates.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOLIPASE A2 INHIBITOR
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7474
Polymers27,5112
Non-polymers2362
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-31 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.049, 54.708, 104.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PHOSPHOLIPASE A2 INHIBITOR


Mass: 13664.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Vipera ammodytes ammodytes (western sand viper)
Species: Vipera ammodytes / Strain: ammodytes / References: UniProt: P04084
#2: Protein PHOSPHOLIPASE A2 / VIPOXIN


Mass: 13846.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence homology between phospholipase and its inhibitor in snake venom. The primary structure of phospholipase A2 of vipoxin from the venom of the Bulgarian viper (Vipera ammodytes ammodytes, Serpentes)
Source: (natural) Vipera ammodytes ammodytes (western sand viper)
Species: Vipera ammodytes / Strain: ammodytes / References: UniProt: P14420, phospholipase A2
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 287 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
25 %(v/v)PEG40001drop
318 %(v/v)MPD1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.908 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: Collimator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.37→20 Å / Num. all: 54019 / Num. obs: 53423 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4 / Num. unique all: 2525 / % possible all: 96.1
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 96.1 %

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOK

1aok


Resolution: 1.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT
Details: used maximum likelihood target using amplitudes procedure
RfactorNum. reflection% reflection
Rfree0.195 5083 10 %
Rwork0.182 --
all-50667 -
obs-50300 99 %
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.126 Å20.732 Å2-1.858 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 336 2247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7

+
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