[English] 日本語
Yorodumi
- PDB-2h4c: Structure of Daboiatoxin (heterodimeric PLA2 venom) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h4c
TitleStructure of Daboiatoxin (heterodimeric PLA2 venom)
Components
  • Phospholipase A2-II
  • Phospholipase A2-III
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / NON-INHIBITOR ACIDIC PLA2 / BASIC PLA2 / HETERODIMER
Function / homology
Function and homology information


phospholipase A2 inhibitor activity / 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 / inflammatory response ...phospholipase A2 inhibitor activity / 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 / inflammatory response / 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 daboiatoxin A chain / Acidic phospholipase A2 daboiatoxin B chain
Similarity search - Component
Biological speciesDaboia russellii siamensis (Siamese Russell's viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGopalan, G. / Thwin, M.M. / Gopalakrishnakone, P. / Swaminathan, K.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Structural and pharmacological comparison of daboiatoxin from Daboia russelli siamensis with viperotoxin F and vipoxin from other vipers.
Authors: Gopalan, G. / Thwin, M.M. / Gopalakrishnakone, P. / Swaminathan, K.
History
DepositionMay 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A2-III
B: Phospholipase A2-II
C: Phospholipase A2-III
D: Phospholipase A2-II
E: Phospholipase A2-III
F: Phospholipase A2-II
G: Phospholipase A2-III
H: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)110,6978
Polymers110,6978
Non-polymers00
Water3,585199
1
A: Phospholipase A2-III
B: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)27,6742
Polymers27,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area12170 Å2
MethodPISA
2
C: Phospholipase A2-III
D: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)27,6742
Polymers27,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-21 kcal/mol
Surface area12450 Å2
MethodPISA
3
E: Phospholipase A2-III
F: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)27,6742
Polymers27,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-18 kcal/mol
Surface area12500 Å2
MethodPISA
4
G: Phospholipase A2-III
H: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)27,6742
Polymers27,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-22 kcal/mol
Surface area11700 Å2
MethodPISA
5
E: Phospholipase A2-III
F: Phospholipase A2-II

G: Phospholipase A2-III
H: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)55,3484
Polymers55,3484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z+2/31
Buried area8120 Å2
ΔGint-52 kcal/mol
Surface area21320 Å2
MethodPISA
6
A: Phospholipase A2-III
B: Phospholipase A2-II

C: Phospholipase A2-III
D: Phospholipase A2-II


Theoretical massNumber of molelcules
Total (without water)55,3484
Polymers55,3484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-2/31
Buried area8250 Å2
ΔGint-52 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.977, 66.977, 240.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Phospholipase A2-III / ACIDIC PHOSPHOLIPASE A2


Mass: 13632.182 Da / Num. of mol.: 4 / Fragment: residues 1-133 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: VENOM / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q7T2R1, phospholipase A2
#2: Protein
Phospholipase A2-II / BASIC PHOSPHOLIPASE A2


Mass: 14042.034 Da / Num. of mol.: 4 / Fragment: residues 1-133 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: VENOM / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q7T3T5, phospholipase A2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: calcium chloride grid screen (Molecular Dimensions), 1.5M CaCl2, Tris-HCl (pH 9.0), 10% (w/v) PEG 4000, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2003
RadiationMonochromator: SILICA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.6→17 Å / Num. obs: 36932 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.074
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.1 % / Rsym value: 0.164 / % possible all: 100

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POA

1poa


Resolution: 2.6→7.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 388459.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.475. TWINNED R VALUE (WORKING SET): 0.212, TWINNED FREE R VALUE: 0.307, TWINNED ...Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.475. TWINNED R VALUE (WORKING SET): 0.212, TWINNED FREE R VALUE: 0.307, TWINNED BIN R VALUE (WORKING SET): 0.311, TWINNED BIN FREE R VALUE: 0.3242
RfactorNum. reflection% reflectionSelection details
Rfree0.307 3169 9.3 %RANDOM
Rwork0.22 ---
obs0.22 33806 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.4634 Å2 / ksol: 0.4559 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å26.25 Å20 Å2
2--1.19 Å20 Å2
3----2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.6→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 0 199 7879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.52
X-RAY DIFFRACTIONc_scangle_it2.282.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 471 8.6 %
Rwork0.311 4987 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

+
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