[English] 日本語
Yorodumi
- PDB-3v99: S663D Stable-5-LOX in complex with Arachidonic Acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v99
TitleS663D Stable-5-LOX in complex with Arachidonic Acid
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE / Lipoxygenase / dioxygenase
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 / Synthesis of Lipoxins (LX) / negative regulation of response to endoplasmic reticulum stress / negative regulation of sprouting angiogenesis / 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 / arachidonic acid metabolic process / negative regulation of vascular wound healing / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / lipid oxidation / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of maresins / regulation of cellular response to oxidative stress / leukotriene metabolic process / negative regulation of wound healing / hepoxilin biosynthetic process / leukocyte migration involved in inflammatory response / Synthesis of Leukotrienes (LT) and Eoxins (EX) / linoleic acid metabolic process / leukotriene biosynthetic process / regulation of reactive oxygen species biosynthetic process / long-chain fatty acid biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / negative regulation of endothelial cell proliferation / regulation of cytokine production involved in inflammatory response / regulation of insulin secretion / humoral immune response / positive regulation of bone mineralization / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / glucose homeostasis / nuclear envelope / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / 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-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, vertebrates, PLAT domain / 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. / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ARACHIDONIC ACID / : / Polyunsaturated fatty acid 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsGilbert, N.C. / Rui, Z. / Neau, D.B. / Waight, M. / Bartlett, S.G. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E.
CitationJournal: Faseb J. / Year: 2012
Title: Conversion of human 5-lipoxygenase to a 15-lipoxygenase by a point mutation to mimic phosphorylation at Serine-663.
Authors: Gilbert, N.C. / Rui, Z. / Neau, D.B. / Waight, M.T. / Bartlett, S.G. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Feb 28, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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_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: Arachidonate 5-lipoxygenase
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3455
Polymers158,9292
Non-polymers4163
Water7,062392
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8253
Polymers79,4641
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,4641
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.755, 200.844, 72.184
Angle α, β, γ (deg.)90.00, 105.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 79464.250 Da / Num. of mol.: 2
Mutation: W14E, F15H, W76G, L77S, C241A, C562A, K654E, K655N, K656L, S664A
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.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACD / ARACHIDONIC ACID / Arachidonic acid


Mass: 304.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP ENTRY P09917 RESIDUES 41-45 (PRO PHE TYR ASN ASP) WERE DELETED AND REPLACED WITH RESIDUES GS(GLY SER)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2010
RadiationMonochromator: Fast monochromatic rotary beam shutters with opening and closing times less than 5 msec, synchronized, precisely with the motion state of the crystallographic spindle
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.25→35.57 Å / Num. all: 62626 / Num. obs: 62626 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID
2.25-2.381
2.39-2.61
2.61-2.911
2.92-3.361
3.37-4.111
4.12-35.571

-
Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.252→35.57 Å / SU ML: 0.61 / σ(F): 0.06 / Phase error: 23.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2000 3.19 %2$
Rwork0.1865 ---
obs0.1879 62613 93.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.012 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8681 Å20 Å2-5.654 Å2
2--7.3154 Å20 Å2
3----9.1835 Å2
Refinement stepCycle: LAST / Resolution: 2.252→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10334 0 24 392 10750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310632
X-RAY DIFFRACTIONf_angle_d0.66114419
X-RAY DIFFRACTIONf_dihedral_angle_d13.2513935
X-RAY DIFFRACTIONf_chiral_restr0.051561
X-RAY DIFFRACTIONf_plane_restr0.0021859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2522-2.30850.31751090.23493315X-RAY DIFFRACTION73
2.3085-2.37090.28631350.21924097X-RAY DIFFRACTION89
2.3709-2.44060.28521370.21424145X-RAY DIFFRACTION90
2.4406-2.51940.24291390.21224200X-RAY DIFFRACTION91
2.5194-2.60940.29211410.20334275X-RAY DIFFRACTION93
2.6094-2.71380.271430.21244356X-RAY DIFFRACTION94
2.7138-2.83730.26521450.20814386X-RAY DIFFRACTION95
2.8373-2.98680.26861460.20694417X-RAY DIFFRACTION96
2.9868-3.17390.22981490.1944504X-RAY DIFFRACTION97
3.1739-3.41870.22371490.1814526X-RAY DIFFRACTION98
3.4187-3.76240.191500.16224561X-RAY DIFFRACTION99
3.7624-4.30610.21391530.15394598X-RAY DIFFRACTION99
4.3061-5.42210.1821500.15564576X-RAY DIFFRACTION99
5.4221-35.5790.22861540.19874657X-RAY DIFFRACTION99
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)
11.2559-0.68720.55081.7482-0.30741.1174-0.0373-0.0320.0587-0.05420.0701-0.22880.120.1325-0.04560.14060.0158-0.02050.0814-0.04560.114723.8382-85.881-2.3355
20.10580.22330.31220.41460.60580.8837-0.05660.0506-0.10840.1411-0.02050.04620.29680.20770.03480.12250.04360.01990.27480.0310.224723.1814-85.171-41.3752
32.15310.09110.0271.15560.02091.0153-0.0071-0.07880.06580.01490.02730.0627-0.0744-0.074-0.00930.0950.0068-0.00960.1023-0.02160.0852-7.0197-70.1133-46.9374
40.0924-0.19840.267-0.1453-0.29931.8690.021-0.0159-0.00610.06120.0139-0.0298-0.1195-0.1323-0.02510.17980.0014-0.00440.0955-0.00540.15454.163-74.3655-27.2401
52.8468-0.4454-3.87794.56070.35086.63490.1906-0.6977-0.47960.4818-0.235-0.38690.25990.2720.07850.1992-0.0334-0.03950.35080.10180.38618.1305-84.2108-41.8144
64.0393-0.0393.50494.7944-2.04875.59620.28930.59130.0066-0.5206-0.13870.0690.71560.8553-0.16390.24650.0429-0.05940.2324-0.00630.253310.12-91.704-13.7646
71.402-0.27180.70681.1535-1.09672.30450.30350.2629-0.3886-0.30430.11670.13470.86870.0219-0.01010.3431-0.0117-0.03920.1676-0.03760.2065-0.3818-92.7962-25.7243
80.86630.46720.05093.2138-1.06482.5468-0.2870.21850.2006-0.50120.1786-0.2429-0.09070.08620.01440.2888-0.09180.01580.1370.03620.1762-9.9631-17.8531-63.7652
90.6396-0.14220.47260.2561-0.190.86180.04140.00660.0150.0338-0.0333-0.03660.05220.0659-0.01290.1719-0.02410.02910.106-0.00830.15894.675-38.1634-26.6041
102.8136-1.1320.71695.5592-1.72914.39130.27970.20590.12790.0452-0.0585-0.30570.14910.4121-0.1610.1996-0.00860.01310.1827-0.07710.19356.9844-40.799-37.9375
111.2899-0.06920.78430.1894-0.08791.16190.0419-0.079-0.1250.00920.0062-0.0065-0.0067-0.0225-0.04290.1719-0.01620.02840.10720.01660.147-3.8376-37.6843-28.2086
127.6635-2.89672.45555.6592-0.31974.3834-0.24390.71460.8189-0.1450.0514-0.24390.1710.16250.22630.2843-0.09250.06350.27560.07630.349212.528-24.3459-32.6137
132.53710.86531.46340.52910.89743.2698-0.20120.32760.4171-0.04290.0632-0.0574-0.78020.07410.13760.2949-0.02310.04650.150.04540.2245-10.6716-20.9362-42.0524
144.5159-0.36712.87371.5112-0.60013.8623-0.3886-0.31550.46810.1341-0.04930.0902-0.5783-0.18090.35020.15020.02170.02670.1035-0.01490.1749-14.0366-19.0066-27.6211
151.6994-0.34570.52451.7727-0.35182.6321-0.3019-0.13840.3521-0.0249-0.0709-0.4492-0.3310.3196-0.45580.1825-0.0776-0.01540.216-0.01180.2335-0.6851-23.5745-25.5104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:162)
2X-RAY DIFFRACTION2chain 'A' and (resseq 163:216)
3X-RAY DIFFRACTION3chain 'A' and (resseq 217:343)
4X-RAY DIFFRACTION4chain 'A' and (resseq 344:597)
5X-RAY DIFFRACTION5chain 'A' and (resseq 598:610)
6X-RAY DIFFRACTION6chain 'A' and (resseq 614:627)
7X-RAY DIFFRACTION7chain 'A' and (resseq 628:672)
8X-RAY DIFFRACTION8chain 'B' and (resseq -8:112)
9X-RAY DIFFRACTION9chain 'B' and (resseq 113:400)
10X-RAY DIFFRACTION10chain 'B' and (resseq 401:442)
11X-RAY DIFFRACTION11chain 'B' and (resseq 443:597)
12X-RAY DIFFRACTION12chain 'B' and (resseq 598:613)
13X-RAY DIFFRACTION13chain 'B' and (resseq 614:627)
14X-RAY DIFFRACTION14chain 'B' and (resseq 628:654)
15X-RAY DIFFRACTION15chain 'B' and (resseq 655:673)

+
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