[English] 日本語
Yorodumi
- PDB-1lwb: Crystal structure of prokaryotic phospholipase A2 at atomic resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lwb
TitleCrystal structure of prokaryotic phospholipase A2 at atomic resolution
Componentsputative secreted protein
KeywordsHYDROLASE / Phospholipase A2 / atomic resolution / internal motion
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / metal ion binding
Similarity search - Function
Phospholipase A2, prokaryotic/fungal / Prokaryotic phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospholipase A2 / Secreted protein
Similarity search - Component
Biological speciesStreptomyces violaceoruber (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMatoba, Y. / Sugiyama, M.
Citation
Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003
Title: Atomic resolution structure of prokaryotic phospholipase A2: Analysis of internal motion and implication for a catalytic mechanism.
Authors: Matoba, Y. / Sugiyama, M.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of prokaryotic phospholipase A2
Authors: Matoba, Y. / Katsube, Y. / Sugiyama, M.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: A novel prokaryotic phospholipase A2. Characterizaton, gene cloning and solution structure
Authors: Sugiyama, M. / Ohtani, K. / Izuhara, M. / Koike, T. / Suzuki, K. / Imamura, S. / Misaki, H.
History
DepositionMay 31, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative secreted protein


Theoretical massNumber of molelcules
Total (without water)13,5711
Polymers13,5711
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.340, 57.495, 31.807
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis enzyme is a monomeric protein in solution.

-
Components

#1: Protein putative secreted protein / Phospholipase A2


Mass: 13570.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces violaceoruber (bacteria) / Plasmid: pIJ680 / Species (production host): Streptomyces lividans / Production host: Streptomyces lividans TK24 (bacteria) / Strain (production host): TK24
References: UniProt: Q9Z4W2, UniProt: Q6UV28*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.48 Å3/Da / Density % sol: 17.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, lithium sulfate, sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 297 K / pH: 8 / Method: vapor diffusion, hanging drop / Details: Matoba, Y., (2002) J.Biol.Chem., 277, 20059.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
220 mM1dropCaCl2
320 mg/mlprotein1drop
414 %(w/v)PEG60001reservoir
50.2 M1reservoirLi2SO4
60.1 Msodium cacodylate1reservoir

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.71073 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 0.923→100 Å / Num. obs: 45532 / % possible obs: 67.48 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.65 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.21
Reflection shellResolution: 0.923→0.954 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 1.64 / Num. unique all: 1418 / % possible all: 22.75
Reflection shell
*PLUS
% possible obs: 22.75 % / Num. unique obs: 1418 / Mean I/σ(I) obs: 5.82

-
Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAZ

1faz


Resolution: 1.05→10 Å / Num. parameters: 10812 / Num. restraintsaints: 13414 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC TEMPERATURE FACTOR WAS INTRODUCED.
RfactorNum. reflection% reflectionSelection details
Rwork0.1034 ---
all0.1034 37649 --
obs0.1034 37649 82.2 %-
Rfree-3423 9.1 %RANDOM
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 844 / Occupancy sum non hydrogen: 1120.7
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 202 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0225
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.128
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.132
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1037 / Rfactor obs: 0.103 / Rfactor Rwork: 0.097
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg20.9
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg2.03

+
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://pdbjlvh1.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