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- PDB-6ns2: Crystal structure of fungal lipoxygenase from Fusarium graminearu... -

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Basic information

Entry
Database: PDB / ID: 6ns2
TitleCrystal structure of fungal lipoxygenase from Fusarium graminearum. P212121 crystal form.
Componentslipoxygenase
KeywordsOXIDOREDUCTASE / lipoxygenase / fungus / Fe coordination
Function / homology
Function and homology information


linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / lipid oxidation / linoleic acid metabolic process / metal ion binding
Similarity search - Function
Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
: / Manganese lipoxygenase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsPakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HL 107887 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RR-15301 United States
CitationJournal: Protein Sci. / Year: 2019
Title: An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere.
Authors: Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipoxygenase
C: lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,9254
Polymers172,8142
Non-polymers1122
Water95553
1
A: lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4632
Polymers86,4071
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4632
Polymers86,4071
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.489, 95.060, 189.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 100 - 745 / Label seq-ID: 124 - 769

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein lipoxygenase


Mass: 86406.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG02216.1, FGRAMPH1_01T05341 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I1REW2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.4 Å3/Da / Density % sol: 48.22 % / Description: Plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 0.05 M proline, 0.1 M imidazole acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7413 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2014
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7413 Å / Relative weight: 1
ReflectionResolution: 2.79→47.58 Å / Num. obs: 40654 / % possible obs: 98.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.072 / Net I/σ(I): 8.2
Reflection shellResolution: 2.79→2.94 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5781 / CC1/2: 0.828 / Rpim(I) all: 0.395 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RDE

3rde


Resolution: 2.79→47.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 41.962 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24943 2015 5 %RANDOM
Rwork0.20547 ---
obs0.20763 38588 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.842 Å2
Baniso -1Baniso -2Baniso -3
1-8.29 Å20 Å2-0 Å2
2---4.36 Å20 Å2
3----3.93 Å2
Refinement stepCycle: 1 / Resolution: 2.79→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10103 0 2 53 10158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01310365
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179411
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.64914081
X-RAY DIFFRACTIONr_angle_other_deg1.131.57721943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92451264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92223.833527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.118151735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4341540
X-RAY DIFFRACTIONr_chiral_restr0.0520.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022102
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8213.2265068
X-RAY DIFFRACTIONr_mcbond_other0.823.2265067
X-RAY DIFFRACTIONr_mcangle_it1.474.8376328
X-RAY DIFFRACTIONr_mcangle_other1.474.8386329
X-RAY DIFFRACTIONr_scbond_it0.6993.2735297
X-RAY DIFFRACTIONr_scbond_other0.6973.2735296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2174.8747753
X-RAY DIFFRACTIONr_long_range_B_refined2.54736.8511478
X-RAY DIFFRACTIONr_long_range_B_other2.54736.85211479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21377 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.792→2.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 146 -
Rwork0.38 2744 -
obs--96.88 %
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)
10.6275-0.1520.37042.6049-0.71752.2020.0268-0.0588-0.07990.1970.0718-0.03890.0484-0.0277-0.09860.2123-0.0438-0.01190.0319-0.03170.117927.733211.5611-0.8559
20.42730.4233-0.3023.7894-1.22763.5105-0.01050.10590.0416-0.7630.0552-0.0437-0.17330.0981-0.04470.3061-0.02520.06390.0759-0.01140.120125.27935.68951.7102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A100 - 745
2X-RAY DIFFRACTION2C100 - 745

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