[English] 日本語
Yorodumi
- PDB-5ek8: Crystal structure of a 9R-lipoxygenase from Cyanothece PCC8801 at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ek8
TitleCrystal structure of a 9R-lipoxygenase from Cyanothece PCC8801 at 2.7 Angstroms
ComponentsLipoxygenase
KeywordsOXIDOREDUCTASE / non-heme iron / PLAT domain / lipoxygenase
Function / homology
Function and homology information


lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding
Similarity search - Function
Transthyretin-like superfamily / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
: / Lipoxygenase domain-containing protein
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsFeussner, I. / Ficner, R. / Neumann, P. / Newie, J. / Andreou, A. / Einsle, O.
Funding support Germany, 3items
OrganizationGrant numberCountry
International Research Training Group (IRTG) 1422 Germany
Fonds of the Chemical Industry (FCI) Germany
Goettingen Graduate School of Neurosciences and Molecular Biology (GGNB) Germany
CitationJournal: J.Lipid Res. / Year: 2016
Title: Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition.
Authors: Newie, J. / Andreou, A. / Neumann, P. / Einsle, O. / Feussner, I. / Ficner, R.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)76,6843
Polymers76,6051
Non-polymers792
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-26 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.166, 121.166, 234.673
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Lipoxygenase / CspLOX1


Mass: 76605.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 8801) (bacteria)
Gene: PCC8801_2437 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Star / References: UniProt: B7K2Q5
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% pentaerythritol propoxylate (5/4 PO/OH), 0.14 M KCl and 50 mM HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.91736, 1.03663
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.917361
21.036631
ReflectionNumber: 536648 / Rmerge(I) obs: 0.175 / Χ2: 0.93 / D res high: 2.8 Å / Num. obs: 47310 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
20301
102092410.026
4.710900610.074
4.44.7222010.087
4.14.4287310.096
3.84.1385010.14
3.53.8529610.213
3.23.5747210.349
3.13.2315510.516
33.1365110.671
2.93411610.939
2.82.9474711.146
ReflectionResolution: 2.7→20 Å / Num. all: 28717 / Num. obs: 28631 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 50.82 Å2 / Rmerge F obs: 0.19 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.091 / Rsym value: 0.099 / Χ2: 0.972 / Net I/av σ(I): 1.8 / Net I/σ(I): 19.6 / Num. measured all: 158532
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRrim(I) all% possible all
2.7-2.84.70.6751.7960740.82499.9
2.8-2.90.5882.1268600.70999.8
2.9-30.4352.4975110.51999.5
3-3.10.2943.6180760.34699.9
3.1-3.410.1965.84292520.22999.8
3.41-3.720.1189.94227460.13899.3
3.72-4.030.07714.65162610.0998.2
4.03-4.340.05221.63124820.0699.7
4.34-4.650.04624.1392960.05499.7
4.65-100.03828.04364680.04499.5
10-200.01756.3335060.0297.8
20-30

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHELXCDphasing
autoSHARPphasing
ARPmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→19.763 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1444 5.05 %Random selection
Rwork0.1986 ---
obs0.201 28582 99.74 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 2 51 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045539
X-RAY DIFFRACTIONf_angle_d0.8237538
X-RAY DIFFRACTIONf_dihedral_angle_d13.9682078
X-RAY DIFFRACTIONf_chiral_restr0.033819
X-RAY DIFFRACTIONf_plane_restr0.004992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79630.35641270.27892625X-RAY DIFFRACTION99
2.7963-2.90790.32141590.27212635X-RAY DIFFRACTION100
2.9079-3.03980.29031280.24822692X-RAY DIFFRACTION100
3.0398-3.19940.28331490.2442648X-RAY DIFFRACTION100
3.1994-3.39890.29821520.22652659X-RAY DIFFRACTION100
3.3989-3.65980.29121620.2212671X-RAY DIFFRACTION100
3.6598-4.02530.23961280.20062734X-RAY DIFFRACTION100
4.0253-4.60140.19341580.15352726X-RAY DIFFRACTION100
4.6014-5.77320.2031460.1632786X-RAY DIFFRACTION100
5.7732-19.76310.2211350.17962962X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0940.0610.41215.4725-3.19281.9029-0.22650.2902-0.3123-0.16580.0099-0.22150.25540.0760.08480.5820.02340.00930.6607-0.02390.567756.2212-5.08137.7865
20.3705-0.66980.35394.7547-3.41122.93530.08680.031-0.04570.1438-0.0242-0.117-0.19670.2029-0.11040.8573-0.002-0.07710.7186-0.01390.583558.189522.868338.0998
31.13490.3967-0.03491.22080.06750.9495-0.18390.21990.41040.0920.0758-0.0132-0.57460.47780.09280.7328-0.2439-0.08540.65540.03120.570562.80736.471519.5255
40.71530.6220.04021.1092-0.02191.1658-0.0343-0.06640.07090.09140.02240.0618-0.014-0.05080.00710.28380.02960.0070.33680.020.319132.91887.595121.6707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:22)
2X-RAY DIFFRACTION2chain A and (resid 23:42)
3X-RAY DIFFRACTION3chain A and (resid 43:165)
4X-RAY DIFFRACTION4chain A and (resid 166:847)

+
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