[English] 日本語
Yorodumi
- PDB-7ttl: Stable-5-LOX elongated Ha2 (4 copies ASU) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ttl
TitleStable-5-LOX elongated Ha2 (4 copies ASU)
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE / Lipoxygenase / dioxygenase / membrane-binding
Function / homology
Function and homology information


arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives ...arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Biosynthesis of DPAn-3-derived maresins / arachidonate 12(S)-lipoxygenase activity / leukocyte chemotaxis involved in inflammatory response / negative regulation of sprouting angiogenesis / Biosynthesis of Lipoxins (LX) / negative regulation of response to endoplasmic reticulum stress / Synthesis of 5-eicosatetraenoic acids / positive regulation of leukocyte adhesion to arterial endothelial cell / lipoxygenase pathway / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Interleukin-18 signaling / dendritic cell migration / arachidonate metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / negative regulation of vascular wound healing / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / lipid oxidation / Biosynthesis of maresins / regulation of cellular response to oxidative stress / leukotriene metabolic process / negative regulation of wound healing / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukocyte migration involved in inflammatory response / leukotriene biosynthetic process / long-chain fatty acid biosynthetic process / regulation of reactive oxygen species biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / regulation of cytokine production involved in inflammatory response / negative regulation of endothelial cell proliferation / humoral immune response / positive regulation of bone mineralization / regulation of insulin secretion / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / nuclear envelope / glucose homeostasis / regulation of inflammatory response / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / iron ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular space / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase ...Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 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.
Similarity search - Domain/homology
: / Polyunsaturated fatty acid 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsGilbert, N.C. / Newcomer, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM143724-01 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Helical remodeling augments 5-lipoxygenase activity in the synthesis of proinflammatory mediators.
Authors: Gallegos, E.M. / Reed, T.D. / Mathes, F.A. / Guevara, N.V. / Neau, D.B. / Huang, W. / Newcomer, M.E. / Gilbert, N.C.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arachidonate 5-lipoxygenase
C: Arachidonate 5-lipoxygenase
D: Arachidonate 5-lipoxygenase
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,9688
Polymers317,7454
Non-polymers2234
Water8,575476
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.791, 204.547, 106.768
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Arachidonate 5-lipoxygenase / 5-lipoxygenase


Mass: 79436.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX5, LOG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P09917, arachidonate 5-lipoxygenase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% Tacsimate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.43→102.27 Å / Num. obs: 217327 / % possible obs: 97.91 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 8.58
Reflection shellResolution: 2.43→2.517 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 11353 / CC1/2: 0.629

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O8Y

3o8y


Resolution: 2.43→102.27 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 3748 1.72 %
Rwork0.2147 213579 -
obs0.2158 217327 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.66 Å2 / Biso mean: 65.339 Å2 / Biso min: 24.82 Å2
Refinement stepCycle: final / Resolution: 2.43→102.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21195 0 4 476 21675
Biso mean--43.69 47.86 -
Num. residues----2607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.460.39831300.35637298742887
2.46-2.490.36581360.35227927806393
2.49-2.520.34831370.34937768790593
2.52-2.560.42211380.33797581771989
2.56-2.60.39961360.3477839797593
2.6-2.640.35621470.32188050819795
2.64-2.680.35441390.31978024816395
2.68-2.730.35971500.30728132828296
2.73-2.780.37021310.29887999813095
2.78-2.830.3991320.29188046817895
2.83-2.890.2871410.28128058819995
2.89-2.950.35621510.27558005815694
2.95-3.020.30991250.28877940806595
3.02-3.10.33451290.27257801793092
3.1-3.180.34521400.27787533767389
3.18-3.270.31051410.23718030817196
3.27-3.380.25481440.20748204834896
3.38-3.50.32171440.20238097824195
3.5-3.640.28031370.17878067820496
3.64-3.810.26431340.17468024815895
3.81-4.010.21551350.16897869800494
4.01-4.260.25461480.14897599774790
4.26-4.590.17871440.13988081822596
4.59-5.050.19431460.14278011815795
5.05-5.780.22081300.17238035816595
5.78-7.280.24841410.19967810795193
7.28-102.270.22411420.18357751789392
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)
13.2590.0651.25860.4138-0.11911.16370.12-0.0963-0.0986-0.0652-0.0414-0.02470.07190.005-0.0880.26650.01630.04590.2658-0.02160.466760.195620.7666156.7285
22.6484-0.9653-0.44092.58220.42451.5220.02640.3641-0.7788-0.26650.1934-0.82950.16340.3085-0.15420.3452-0.02190.09160.4596-0.16520.844576.61369.4458106.5796
37.7276-0.53222.03140.0725-0.23481.72650.10851.1097-0.9425-0.05950.1914-0.16010.12290.234-0.25250.4033-0.04110.09090.57060.05130.386753.092122.296695.106
42.9558-0.14230.17860.671-0.09120.39170.01830.290.0987-0.1370.00320.12920.0313-0.0722-0.01660.2585-0.01960.01720.25790.01470.296835.150426.9821109.0387
52.9016-0.41461.3820.9013-0.7031.25810.08150.3215-0.3993-0.1414-0.00710.07090.10730.0184-0.10030.29650.0130.06130.2984-0.1160.350639.024415.9579108.241
62.2012-0.62920.58161.8447-0.66381.08020.02770.19190.3879-0.15690.28830.5989-0.0606-0.3227-0.24060.398-0.0192-0.01780.48210.21991.25134.108477.6216103.265
71.5388-0.42070.1690.7253-0.01710.53940.03490.16750.6779-0.1148-0.1788-0.3392-0.08920.21870.14180.3652-0.04150.03840.40650.18370.813750.192259.8104105.7645
82.1312-1.74710.46074.4151.12462.65010.09360.40580.3587-0.58870.0153-0.4999-0.1390.5406-0.16450.352-0.0722-0.00990.49670.21990.910431.268861.8131100.6948
91.804-0.430.17740.60920.03020.3968-0.01410.10430.8378-0.0849-0.0163-0.0639-0.1310.06140.02640.384-0.0349-0.04610.3660.13551.012637.758968.6498111.0844
102.0575-0.198-0.3231.39770.16390.90220.03120.28250.3186-0.53750.23351.1061-0.2567-0.2751-0.20410.4897-0.0099-0.07050.49240.23641.737324.973387.1669154.1644
112.18540.02880.02491.8978-0.33050.42750.05710.24730.2622-0.3443-0.0509-0.13360.03730.1176-0.02570.4162-0.03830.04240.43390.02660.935862.297769.9539154.9058
122.49310.03-0.30191.9604-0.32750.70150.04030.13820.3545-0.2066-0.0516-0.1970.00520.01530.00570.33230.005-0.00630.33870.05710.858561.211269.3196159.5408
134.264-0.4405-0.07062.08040.26421.32450.07090.1814-0.5895-0.19210.0939-0.54420.1580.1923-0.13220.3109-0.01840.05310.3903-0.09520.779295.895717.3277153.9037
146.78133.92773.94583.39662.3182.2357-0.07550.7733-0.2381-0.26390.204-0.73880.08080.4516-0.19350.39440.00290.07760.4412-0.00750.270566.73520.5302140.3895
150.6151-0.6462-0.7532.33342.08994.1008-0.0873-0.1728-0.04460.1008-0.02610.15560.11660.02060.16350.202-0.0198-0.01050.3770.00760.600841.222529.1928158.6549
163.9713-0.48240.18921.07980.10040.32360.0282-0.05410.3186-0.0449-0.0278-0.0002-0.03680.02710.02170.259-0.01070.03460.2535-0.04070.43862.548932.5908161.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 532 through 673 )B532 - 673
2X-RAY DIFFRACTION2chain 'A' and (resid -12 through 141 )A-12 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 187 )A142 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 531 )A188 - 531
5X-RAY DIFFRACTION5chain 'A' and (resid 532 through 673 )A532 - 673
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 141 )C5 - 141
7X-RAY DIFFRACTION7chain 'C' and (resid 142 through 385 )C142 - 385
8X-RAY DIFFRACTION8chain 'C' and (resid 386 through 442 )C386 - 442
9X-RAY DIFFRACTION9chain 'C' and (resid 443 through 673 )C443 - 673
10X-RAY DIFFRACTION10chain 'D' and (resid -12 through 112 )D-12 - 112
11X-RAY DIFFRACTION11chain 'D' and (resid 113 through 285 )D113 - 285
12X-RAY DIFFRACTION12chain 'D' and (resid 286 through 673 )D286 - 673
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 151 )B5 - 151
14X-RAY DIFFRACTION14chain 'B' and (resid 152 through 196 )B152 - 196
15X-RAY DIFFRACTION15chain 'B' and (resid 197 through 289 )B197 - 289
16X-RAY DIFFRACTION16chain 'B' and (resid 290 through 531 )B290 - 531

+
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