[English] 日本語
Yorodumi
- PDB-1qll: Piratoxin-II (Prtx-II) - a K49 PLA2 from Bothrops pirajai -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qll
TitlePiratoxin-II (Prtx-II) - a K49 PLA2 from Bothrops pirajai
ComponentsPHOSPHOLIPASE A2
KeywordsNEUROTOXIN / K49 PHOSPHOLIPASE A2 (PLA2)
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / toxin activity / 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
N-TRIDECANOIC ACID / Basic phospholipase A2 homolog piratoxin-2
Similarity search - Component
Biological speciesBOTHROPS PIRAJAI (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLee, W.-H. / Polikarpov, I.
CitationJournal: Biochemistry / Year: 2001
Title: Structural Basis for Low Catalytic Activity in Lys49 Phospholipases A2-A Hypothesis: The Crystal Structure of Piratoxin II Complexed to Fatty Acid
Authors: Lee, W.H. / Da Silva Giotto, M.T. / Marangoni, S. / Toyama, M.H. / Polikarpov, I. / Garratt, R.C.
History
DepositionSep 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: 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: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9974
Polymers27,5682
Non-polymers4292
Water5,441302
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint0.2 kcal/mol
Surface area16300 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.190, 60.360, 58.740
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.0003, -0.0043), (-0.0003, -0.9999, -0.0157), (-0.0043, 0.0157, -0.9999)
Vector: -0.025, 43.0776, -0.399)
DetailsTHE ASYMMETRIC UNIT CONTAINS A HOMO-DIMERIC COMPLEX

-
Components

#1: Protein PHOSPHOLIPASE A2 / MYOTOXIN II / BOTHROPSTOXIN I / BTXTX1 / BTHTX1


Mass: 13784.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FATTY ACID TRAPPED AT THE HYDROPHOBIC CHANNEL / Source: (natural) BOTHROPS PIRAJAI (snake) / Secretion: TOTAL VENOM / References: UniProt: P82287, phospholipase A2
#2: Chemical ChemComp-TDA / N-TRIDECANOIC ACID


Mass: 214.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PHOSPHOLIPASES A2 (PLA2) CAN BE DIVIDED INTO TWO MAJOR CLASSES BASED UPON CATALYTIC ACTIVITY. ...THE PHOSPHOLIPASES A2 (PLA2) CAN BE DIVIDED INTO TWO MAJOR CLASSES BASED UPON CATALYTIC ACTIVITY. THE D49 CLASS IS ACTIVE, WHILE THE K49 CLASS IS INACTIVE. THE SEQUENCE NUMBERING IS BASED ON A REPRESENTATIVE PHOSPHOLIPASE A2. IN THE K49 PLA2 CLASS ENZYME STUDIED HERE THE LYS IS RESIDUE 48. SIGNIFICANTLY THIS K49 ENZYME, DESPITE ITS LACK OF PHOSPHOLIPASE ACTION, SHOWS SEVERAL PHARMACOLOGICAL EFFECTS. THE STRUCTURE REVEALS THE PRESENCE OF A FATTY ACID MOLECULE TRAPPED IN THE REACTION SITE OF EACH ENZYME MOLECULE.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 28% PEG 3350, 0.25 M LITHIUM SULFATE 0.1 M TRIS-HCL PH 8.5, AT 277 K FOR APPROX. 40 DAYS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
228 %PEG33501reservoir
30.25 M1reservoirLi2SO4
40.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.04→20 Å / Num. obs: 6934 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 3.43 % / Rsym value: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 1.53 % / Mean I/σ(I) obs: 2.57 / Rsym value: 0.26 / % possible all: 72.5
Reflection
*PLUS
Num. measured all: 23809 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 72.5 % / Rmerge(I) obs: 0.26

-
Processing

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

1clp


Resolution: 2.04→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE C-TERMINAL IS CLEARLY VISIBLE IN THE DENSITY MAP AND IT IS MAKING A DISULPHIDE BRIDGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1190 5 %RANDOM
Rwork0.176 ---
obs-23809 90.2 %-
Refinement stepCycle: LAST / Resolution: 2.04→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 30 302 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
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: 0.176
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