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- PDB-5t5v: LIPOXYGENASE-1 (SOYBEAN) AT 293K -

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Basic information

Entry
Database: PDB / ID: 5t5v
TitleLIPOXYGENASE-1 (SOYBEAN) 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 / molecular replacement / Resolution: 1.8 Å
AuthorsPoss, E.M. / Fraser, J.S.
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/Office of the Director1S10OD020062-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM025765 United States
CitationJournal: ACS Cent Sci / Year: 2017
Title: Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling.
Authors: Offenbacher, A.R. / Hu, S. / Poss, E.M. / Carr, C.A.M. / Scouras, A.D. / Prigozhin, D.M. / Iavarone, A.T. / Palla, A. / Alber, T. / Fraser, J.S. / Klinman, J.P.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_detector / pdbx_audit_support
Item: _diffrn_detector.detector / _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 25, 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_ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,1564
Polymers189,0442
Non-polymers1122
Water17,943996
1
A: Seed linoleate 13S-lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5782
Polymers94,5221
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)94,5782
Polymers94,5221
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.572, 92.754, 100.919
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 94522.156 Da / Num. of mol.: 2
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-FE / FE (III) ION / Iron


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.: 996 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.63 % / Mosaicity: 0.09 °
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG-3350, Sodium Acetate

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.8266 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.8→92.754 Å / Num. obs: 154694 / Redundancy: 4.6 % / Biso Wilson estimate: 18.98 Å2 / Rsym value: 0.113 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.94.70.8860.8198.8
1.9-2.014.70.5411.4199
2.01-2.154.70.3422.2199.2
2.15-2.324.70.2243.3199.4
2.32-2.554.60.1624.6199.6
2.55-2.854.60.1156.4199.7
2.85-3.294.60.0788.9199.8
3.29-4.024.50.05112.5199.8
4.02-5.694.40.03318.1199.5
5.69-92.7544.70.02718.51100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10PRE_2104refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZW

3pzw


Resolution: 1.8→91.38 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 17.46
RfactorNum. reflection% reflection
Rfree0.171 1994 1.29 %
Rwork0.134 --
obs0.135 154489 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→91.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13094 0 2 996 14092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121600
X-RAY DIFFRACTIONf_angle_d1.0330098
X-RAY DIFFRACTIONf_dihedral_angle_d10.61713905
X-RAY DIFFRACTIONf_chiral_restr0.0583432
X-RAY DIFFRACTIONf_plane_restr0.0083946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.30361260.277410698X-RAY DIFFRACTION98
1.845-1.89490.26491440.239710825X-RAY DIFFRACTION99
1.8949-1.95070.26521590.208810800X-RAY DIFFRACTION99
1.9507-2.01360.20191360.181710847X-RAY DIFFRACTION99
2.0136-2.08560.20891470.168210797X-RAY DIFFRACTION99
2.0856-2.16910.20781340.153910885X-RAY DIFFRACTION99
2.1691-2.26790.14391450.137110864X-RAY DIFFRACTION99
2.2679-2.38740.17631500.12410893X-RAY DIFFRACTION99
2.3874-2.5370.16791430.123810895X-RAY DIFFRACTION99
2.537-2.73290.18681450.126410946X-RAY DIFFRACTION100
2.7329-3.0080.14951450.128510932X-RAY DIFFRACTION100
3.008-3.44320.18821360.121311012X-RAY DIFFRACTION100
3.4432-4.33810.12871370.094911011X-RAY DIFFRACTION100
4.3381-91.49260.12491470.109511090X-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)
10.17320.0590.07320.0697-0.02060.06620.03940.1646-0.06250.0112-0.06490.12970.0519-0.1142-00.1301-0.0033-0.00260.1946-0.04990.2593-18.3208-44.089632.8865
20.5796-0.0830.01260.101-0.02350.10520.01440.02480.0120.0192-0.0360.08880.0111-0.0288-0.00030.10310.00150.00460.1158-0.00530.1844-11.0658-41.702238.4676
30.7320.2143-0.06620.3058-0.01530.12710.0011-0.002-0.1111-0.01670.0045-0.04410.0040.05160.03630.1061-0.01460.00320.10440.00420.071233.3035-48.013538.9033
40.9530.0974-0.07790.34640.07460.1599-0.00530.04140.1455-0.03730.0090.0394-0.02520.0362-0.00880.0972-0.0158-0.00070.0760.01330.080720.9395-36.146738.3445
50.22750.07750.07930.1385-0.06920.09460.0350.1674-0.0392-0.0389-0.05620.12540.0772-0.05700.13620.0198-0.010.1913-0.02470.2142-21.472-41.915480.6115
60.61250.21660.11670.08940.07540.08160.0496-0.136-0.1020.0379-0.02710.12260.0166-0.0549-0.00260.12940.00510.00670.13550.00880.1405-6.8796-45.149893.7743
70.7766-0.1097-0.00620.1777-0.01790.06950.0476-0.0083-0.1002-0.0225-0.0353-0.00360.00180.02590.00420.1362-0.0044-0.00710.10890.00060.074927.1557-48.810885.1821
81.0476-0.0934-0.0290.27520.07720.17750.0451-0.04840.0785-0.0163-0.0293-0.0053-0.02630.01330.01070.11530.00440.00050.0818-0.00760.059521.1412-37.722590.4819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 66 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 67 THROUGH 190 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 191 THROUGH 496 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 497 THROUGH 839 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 5 THROUGH 93 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 94 THROUGH 221 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 222 THROUGH 409 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 410 THROUGH 839 )

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