[English] 日本語
Yorodumi
- PDB-6ns3: Crystal structure of fungal lipoxygenase from Fusarium graminearu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ns3
TitleCrystal structure of fungal lipoxygenase from Fusarium graminearum. I222 crystal form.
Componentslipoxygenase
KeywordsOXIDOREDUCTASE / lipoxygenase / fungus / Fe coordination
Function / homology
Function and homology information


linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / lipid oxidation / linoleic acid metabolic process / metal ion binding
Similarity search - Function
Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
: / Manganese lipoxygenase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsPakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HL 107887 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RR-15301 United States
CitationJournal: Protein Sci. / Year: 2019
Title: An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere.
Authors: Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4632
Polymers86,4071
Non-polymers561
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.931, 95.537, 186.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein lipoxygenase


Mass: 86406.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG02216.1, FGRAMPH1_01T05341 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I1REW2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.43 Å3/Da / Density % sol: 49.5 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 11% PEG3350, 0.35 M calcium chloride, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 18, 2017 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38079 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 19682 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.972 / Rpim(I) all: 0.062 / Net I/σ(I): 12.2
Reflection shellResolution: 2.84→2.92 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1550 / CC1/2: 0.911 / Rpim(I) all: 0.3 / % possible all: 78.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RDE

3rde


Resolution: 2.84→47.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 60.285 / SU ML: 0.466 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 597 3 %RANDOM
Rwork0.23408 ---
obs0.23524 19085 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0 Å2
2--2.87 Å20 Å2
3----4 Å2
Refinement stepCycle: 1 / Resolution: 2.84→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 1 8 5049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174693
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.6497026
X-RAY DIFFRACTIONr_angle_other_deg1.0581.57710941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56523.84263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02315863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9371520
X-RAY DIFFRACTIONr_chiral_restr0.0390.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4224.042530
X-RAY DIFFRACTIONr_mcbond_other0.4224.042529
X-RAY DIFFRACTIONr_mcangle_it0.7426.063159
X-RAY DIFFRACTIONr_mcangle_other0.7426.063160
X-RAY DIFFRACTIONr_scbond_it0.2944.0452642
X-RAY DIFFRACTIONr_scbond_other0.2844.0452640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5156.0563867
X-RAY DIFFRACTIONr_long_range_B_refined1.47647.2615843
X-RAY DIFFRACTIONr_long_range_B_other1.47347.2585842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.839→2.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 31 -
Rwork0.466 1200 -
obs--84.14 %
Refinement TLS params.Method: refined / Origin x: -29.7567 Å / Origin y: -35.4911 Å / Origin z: -26.0961 Å
111213212223313233
T0.4339 Å2-0.1195 Å20.2625 Å2-0.0722 Å2-0.0999 Å2--0.1969 Å2
L1.4031 °2-0.0207 °2-1.9381 °2-3.0517 °20.2721 °2--5.2057 °2
S0.257 Å °-0.238 Å °0.2957 Å °-0.4292 Å °0.2006 Å °-0.4729 Å °-0.4724 Å °0.5287 Å °-0.4576 Å °

+
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