[English] 日本語
Yorodumi
- PDB-5tqn: Lipoxygenase-1 (soybean) L546A mutant at 293K -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tqn
TitleLipoxygenase-1 (soybean) L546A mutant at 293K
ComponentsSeed linoleate 13S-lipoxygenase-1
KeywordsOXIDOREDUCTASE / lipoxygenase / hydrogen tunneling
Function / homology
Function and homology information


linolenate 9R-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-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 oxidation / fatty acid biosynthetic process / iron 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 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPoss, E.M. / Fraser, J.S. / Gee, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113432 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR022393-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM025765 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.
Authors: Hu, S. / Offenbacher, A.R. / Thompson, E.M. / Gee, C.L. / Wilcoxen, J. / Carr, C.A.M. / Prigozhin, D.M. / Yang, V. / Alber, T. / Britt, R.D. / Fraser, J.S. / Klinman, J.P.
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Seed linoleate 13S-lipoxygenase-1
B: Seed linoleate 13S-lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,0724
Polymers188,9602
Non-polymers1122
Water12,809711
1
A: Seed linoleate 13S-lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5362
Polymers94,4801
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Seed linoleate 13S-lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5362
Polymers94,4801
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.519, 92.656, 100.751
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Seed linoleate 13S-lipoxygenase-1 / Lipoxygenase-1 / L-1


Mass: 94480.078 Da / Num. of mol.: 2 / Mutation: L546A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: LOX1.1, LOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08170, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidue 160 is a Glutamine, as per the obvious electron density at that position

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG-3350, Sodium Acetate

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.826561 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826561 Å / Relative weight: 1
ReflectionResolution: 1.8→45.68 Å / Num. obs: 154946 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.518 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.10pre_2104refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZW

3pzw


Resolution: 1.8→42.966 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.57
RfactorNum. reflection% reflection
Rfree0.168 7855 5.07 %
Rwork0.145 --
obs0.1461 154946 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 187.73 Å2 / Biso mean: 32.5354 Å2 / Biso min: 9.1 Å2
Refinement stepCycle: final / Resolution: 1.8→42.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13069 0 2 724 13795
Biso mean--27.12 32.15 -
Num. residues----1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521448
X-RAY DIFFRACTIONf_angle_d0.74729700
X-RAY DIFFRACTIONf_chiral_restr0.0473283
X-RAY DIFFRACTIONf_plane_restr0.0053930
X-RAY DIFFRACTIONf_dihedral_angle_d10.27513314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.31545010.3071960110102100
1.8205-1.84190.32395250.2999961010135100
1.8419-1.86430.31445550.2862977710332100
1.8643-1.88790.29844990.2743968010179100
1.8879-1.91280.29135420.2582963310175100
1.9128-1.9390.29055430.246961810161100
1.939-1.96670.23925150.2263965110166100
1.9667-1.9960.23365510.2093961510166100
1.996-2.02720.23675390.2069966310202100
2.0272-2.06050.2125530.1941961210165100
2.0605-2.0960.19535160.1797970910225100
2.096-2.13410.2094740.1717973510209100
2.1341-2.17520.18395100.1617965710167100
2.1752-2.21960.16824690.1549969110160100
2.2196-2.26780.18885150.1507968310198100
2.2678-2.32060.16754270.143979410221100
2.3206-2.37860.17374650.1364970910174100
2.3786-2.44290.16274790.1412975910238100
2.4429-2.51480.17775300.136963410164100
2.5148-2.59590.16175520.1346963810190100
2.5959-2.68870.16625630.1425960610169100
2.6887-2.79630.17094880.1374974610234100
2.7963-2.92360.16974940.1407966010154100
2.9236-3.07770.17964900.1403970210192100
3.0777-3.27040.17235590.1378966810227100
3.2704-3.52280.1416010.1197958510186100
3.5228-3.87720.12334360.0981972110157100
3.8772-4.43770.10486010.0893959010191100
4.4377-5.58910.10435590.09395621012199
5.5891-42.97810.13774390.130895831002298
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)
11.6174-0.06850.21610.0811-0.06310.21370.09920.0406-0.1924-0.0256-0.0477-0.12520.04090.0624-0.00010.1868-0.01-0.01090.1723-0.00010.2168141.1111-47.060611.2197
21.25890.21540.03930.4622-0.09340.41840.1125-0.0461-0.11520.023-0.0892-0.00860.0389-0.0283-0.05770.1962-0.0225-0.00730.1560.00790.104198.7013-47.863914.8992
31.73760.2052-0.04290.4522-0.10510.30960.08460.02320.08660.0438-0.0597-0.0235-0.0333-0.0250.01030.1685-0.0216-0.00370.11340.01550.0907111.7917-38.652410.9137
40.6926-0.11810.21980.22990.15330.24030.0452-0.3131-0.05430.145-0.0895-0.1895-0.01010.1214-0.00010.17860.0044-0.00920.24390.0360.2696147.9013-44.621669.1331
50.5488-0.23230.0860.1278-0.08120.1362-0.00680.08990.0967-0.0101-0.0147-0.1346-0.01960.0417-0.00040.13190.00010.01770.12410.00510.2171138.3591-41.892156.9551
61.1067-0.2785-0.11680.3742-0.02460.1865-0.015-0.0445-0.1330.03880.02060.03250.0144-0.07330.02260.1530.0264-0.00050.1491-0.00930.093899.5079-48.995561.1961
71.3543-0.1505-0.07930.4118-0.07030.2686-0.0128-0.05860.13370.03530.0081-0.0328-0.0578-0.06160.01190.12940.03180.00080.1032-0.0130.0901107.3327-38.538261.7069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 244 )A6 - 244
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 452 )A245 - 452
3X-RAY DIFFRACTION3chain 'A' and (resid 453 through 839 )A453 - 839
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 114 )B6 - 114
5X-RAY DIFFRACTION5chain 'B' and (resid 115 through 190 )B115 - 190
6X-RAY DIFFRACTION6chain 'B' and (resid 191 through 442 )B191 - 442
7X-RAY DIFFRACTION7chain 'B' and (resid 443 through 839 )B443 - 839

+
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