[English] 日本語
Yorodumi
- PDB-2fnq: Insights from the X-ray crystal structure of coral 8R-lipoxygenas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fnq
TitleInsights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via A C2-like domain and a structural basis of product chirality
ComponentsAllene oxide synthase-lipoxygenase protein
KeywordsOXIDOREDUCTASE / beta-barrel / eicosanoid / fatty acid / c2-like domain
Function / homology
Function and homology information


arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / iron ion binding / heme binding / membrane / cytoplasm
Similarity search - Function
Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase-1 ...Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase-1 / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Catalase superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Allene oxide synthase-lipoxygenase protein
Similarity search - Component
Biological speciesPlexaura homomalla (black sea rod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsOldham, M.L. / Brash, A.R. / Newcomer, M.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality.
Authors: Oldham, M.L. / Brash, A.R. / Newcomer, M.E.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 28, 2006ID: 1ZQ4
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Allene oxide synthase-lipoxygenase protein
B: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,22710
Polymers159,8752
Non-polymers3528
Water00
1
A: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1145
Polymers79,9381
Non-polymers1764
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1145
Polymers79,9381
Non-polymers1764
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.554, 78.023, 176.490
Angle α, β, γ (deg.)90.00, 96.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains a dimer but the protein in solution is a monomer

-
Components

#1: Protein Allene oxide synthase-lipoxygenase protein


Mass: 79937.531 Da / Num. of mol.: 2 / Fragment: Arachidonate 8-lipoxygenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plexaura homomalla (black sea rod) / Production host: Escherichia coli (E. coli) / References: UniProt: O16025, arachidonate 8-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, IMIDAZOLE ACETATE, SUCROSE, CALCIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 23, 2003
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→29.4 Å / Num. all: 29161 / Num. obs: 28928 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.2→3.4 Å / % possible all: 82.6

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1419 4.5 %RANDOM
Rwork0.254 ---
all0.258 29161 --
obs0.254 28928 92.3 %-
Solvent computationBsol: 43.333 Å2
Displacement parametersBiso mean: 42.633 Å2
Baniso -1Baniso -2Baniso -3
1--16.564 Å20 Å2-6.555 Å2
2---0.482 Å20 Å2
3---17.045 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10426 0 8 0 10434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.434 197 -
Rwork0.36 --
obs-2016 82.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

+
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