[English] 日本語
Yorodumi
- PDB-1lnh: LIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lnh
TitleLIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN
ComponentsLIPOXYGENASE-3
KeywordsOXIDOREDUCTASE / METALLOPROTEIN / FE(II) COMPLEX
Function / homology
Function and homology information


linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 ...Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / 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. / Nuclear Transport Factor 2; Chain: A, / Few Secondary Structures / Irregular / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSkrzypczak-Jankun, E.
Citation
Journal: Proteins / Year: 1997
Title: Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme.
Authors: Skrzypczak-Jankun, E. / Amzel, L.M. / Kroa, B.A. / Funk Jr., M.O.
#1: Journal: J.Mol.Struct. / Year: 1996
Title: Lipoxygenase-A Molecular Complex with a Non-Heme Iron
Authors: Skrzypczak-Jankun, E. / Funk Junior, M.O. / Boyington, J.C. / Amzel, L.M.
#2: Journal: Biochemistry / Year: 1994
Title: Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3
Authors: Kramer, J.A. / Johnson, K.R. / Dunham, W.R. / Sands, R.H. / Funk Junior, M.O.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Characterization of a Soybean Seed Lipoxygenase
Authors: Stallings, W.C. / Kroa, B.A. / Carroll, R.T. / Metzger, A.L. / Funk, M.O.
History
DepositionMar 29, 1996Processing site: BNL
Revision 1.0Feb 2, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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_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: LIPOXYGENASE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9752
Polymers96,9191
Non-polymers561
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.800, 137.400, 61.850
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein LIPOXYGENASE-3 /


Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Strain: PROVAR CULTIVAR / References: UniProt: P09186
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE NUMBERING OF THE SECONDARY STRUCTURE ELEMENTS HAS SYMBOLS AFTER SOYBEAN LIPOXYGENASE L1 AS IN ...THE NUMBERING OF THE SECONDARY STRUCTURE ELEMENTS HAS SYMBOLS AFTER SOYBEAN LIPOXYGENASE L1 AS IN PDB ENTRY 2SBL (BOYINGTON ET AL., 1993, SCIENCE, 260, 1482-1486). THERE ARE SOME KINKS IN 3 HELICES: H2 - AT 283, H9 - AT 521-522, H18 - AT 706, 714-715.
Nonpolymer detailsTHE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 AND ILE 857(C-TERMINAL) THAT ARE ...THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 AND ILE 857(C-TERMINAL) THAT ARE COVALENTLY BOUND TO IRON FE 858, WHILE ASN 713 AND H2O 901 ARE IN A DISTANCE GREATER THAN THE SUM OF THE VAN DER WAALS RADII.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.3 / Details: pH 5.3
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlL31drop1
20.1 MTris-HCl1drop1pH7.0
320 %(w/v)PEG80001drop2
40.05 Msodium citrate phosphate1drop2pH4.6
50.2 %(w/v)1drop2NaN3
60.1 Msodium phosphate1drop3pH7.0
820 %PEG80001reservoir
7water1drop4

-
Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→61.6 Å / Num. obs: 23403 / % possible obs: 80.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.6→2.75 Å / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 3.39 / % possible all: 43.6
Reflection
*PLUS
Num. measured all: 74331
Reflection shell
*PLUS
% possible obs: 48 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MSCdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER ...Starting model: FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER IN PDB BY 2SBL WITH BETTER REFINED MODEL).

1sbl

1sbl

2sbl


Resolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.265 --
Rwork0.174 --
obs0.174 22402 82.1 %
Displacement parametersBiso mean: 31.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 1 170 6867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54

+
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