[English] 日本語
Yorodumi
- PDB-1fb2: STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fb2
TitleSTRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95
ComponentsPHOSPHOLIPASE A2
KeywordsTOXIN / Phospholipase A2 / Daboia Russelli Pulchella / Neurotoxic
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 / 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
Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChandra, V. / Kaur, P. / Betzel, C. / Singh, T.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution.
Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Three-Dimensional Structure of a Presynaptic Neurotoxic Phospholipase A2 from Daboia Russelli pulchella at 2.4 Resolution
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / P Singh, T.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)27,2602
Polymers27,2602
Non-polymers00
Water3,837213
1
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.100, 88.050, 79.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: pulchella / Keywords: NATIVE / References: UniProt: P59071
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM Sodium Cacodylate, 1.4M Ammonium Sulphate, 4mM Calcium Chloride, 3% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
220 mMsodium cacodylate1droppH6.5
31.4 Mammonium sulfate1reservoir
43 %dioxane1reservoir

-
Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→24.1 Å / Num. all: 19822 / Num. obs: 18001 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.026 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1913 / Rsym value: 0.165 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 17922 / % possible obs: 91 % / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.163

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL5

1cl5


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used restrained least-squares refinement procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.272 863 4.8 %Random
Rwork0.216 ---
all0.234 17985 --
obs0.226 17922 90.9 %-
Displacement parametersBiso mean: 42.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 0 213 2101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_bond_d0.006
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23

+
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