[English] 日本語
Yorodumi
- PDB-1pp2: THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pp2
TitleTHE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER
ComponentsCALCIUM-FREE PHOSPHOLIPASE A2
KeywordsHYDROLASE
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
Acidic phospholipase A2
Similarity search - Component
Biological speciesCrotalus atrox (western diamondback rattlesnake)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrunie, S. / Sigler, P.B.
Citation
Journal: J.Biol.Chem. / Year: 1985
Title: The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center.
Authors: Brunie, S. / Bolin, J. / Gewirth, D. / Sigler, P.B.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: A Comparison of the Crystal Structures of Phospholipase A2 from Bovine Pancreas and Crotalus Atrox Venom
Authors: Renetseder, R. / Brunie, S. / Dijkstra, B.W. / Drenth, J. / Sigler, P.B.
#2: Journal: J.Biol.Chem. / Year: 1981
Title: The 2.5 Angstroms Crystal Structure of a Dimeric Phospholipase A2 from the Venom of Crotalus Atrox
Authors: Keith, C. / Feldman, D.S. / Deganello, S. / Glick, J. / Ward, K.B. / Jones, E.O. / Sigler, P.B.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: Characterization of Crystals of Two Venom Phospholipases A2
Authors: Pasek, M. / Keith, C. / Feldman, D. / Sigler, P.B.
History
DepositionMar 10, 1986Processing site: BNL
Revision 1.0May 7, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: CALCIUM-FREE PHOSPHOLIPASE A2
L: CALCIUM-FREE PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)27,2152
Polymers27,2152
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-18 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 100.200, 48.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.12725, 0.1029, -0.98652), (0.09793, -0.98844, -0.11573), (-0.98702, -0.11134, 0.1157)
Vector: 61.65457, 79.66322, 62.94765)
DetailsTHE ENZYME IS A DIMER COMPOSED OF TWO IDENTICAL SUBUNITS OF 122 RESIDUES EACH. THE *RIGHT* SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIER *R*. THE *LEFT* SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIER *L*. THE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE *RIGHT* SUBUNIT (CHAIN *R*) WHEN APPLIED TO THE *LEFT* SUBUNIT (CHAIN *L*).

-
Components

#1: Protein CALCIUM-FREE PHOSPHOLIPASE A2


Mass: 13607.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crotalus atrox (western diamondback rattlesnake)
References: UniProt: P00624, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM11NaCl
210 mMTris-HCl11
40.1 mM11CaCl2
510 mM12Na2EDTA
60.1 mM12CaCl2
3phospholipase A2 solution11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.178 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 137 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.028
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4
X-RAY DIFFRACTIONp_planar_d
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
Refinement
*PLUS
σ(I): 2
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