[English] 日本語
Yorodumi
- PDB-3fg5: Crystal structure determination of a ternary complex of phospholi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fg5
TitleCrystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution
Components
  • Group II Phospholipase A2
  • pentapeptide FLSYK
KeywordsHYDROLASE / pla2 / pentapeptide / FLSYK / ajmaline / ternary complex
Function / homologyPhospholipase A2 / Phospholipase A2 domain / Up-down Bundle / Mainly Alpha / AJMALINE
Function and homology information
Biological speciesDaboia russelli pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumar, M. / Kumar, S. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution
Authors: Kumar, M. / Kumar, S. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Group II Phospholipase A2
C: pentapeptide FLSYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5863
Polymers14,2882
Non-polymers2981
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-2 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.949, 52.949, 48.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Group II Phospholipase A2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russelli pulchella (snake) / References: phospholipase A2
#2: Protein/peptide pentapeptide FLSYK


Mass: 657.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED SHORT PEPTIDE
#3: Chemical ChemComp-AJM / AJMALINE / Ajmaline


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2 / Comment: antiarrhythmic, alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF ENTITY 1 IS THE SAME WITH UNP P59071 PA28_DABRP, WHICH HAS DIFFERENT SOURCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M AMMONIUM SULPHATE, 0.2M AMMONIUM ACETATE, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 2007 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 4639 / Num. obs: 4392 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.439 / % possible all: 98.5

-
Processing

Software
NameClassification
DENZOdata reduction
MOLREPphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZR8

1zr8


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 247 -RANDOM
Rwork0.1876 ---
all0.227 4639 --
obs0.188 4392 93.2 %-
Displacement parametersBiso max: 98.14 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.218 Å20 Å20 Å2
2---1.218 Å20 Å2
3---2.436 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 22 61 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5741.5
X-RAY DIFFRACTIONc_scbond_it2.1422
X-RAY DIFFRACTIONc_mcangle_it2.7022
X-RAY DIFFRACTIONc_scangle_it3.3212.5

+
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