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- PDB-5mee: Cyanothece lipoxygenase 2 (CspLOX2) variant - L304V -

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Basic information

Entry
Database: PDB / ID: 5mee
TitleCyanothece lipoxygenase 2 (CspLOX2) variant - L304V
ComponentsArachidonate 15-lipoxygenase
KeywordsOXIDOREDUCTASE / Linoleate 11-lipoxygenase
Function / homology
Function and homology information


arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipid oxidation / metal ion binding
Similarity search - Function
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.
Similarity search - Domain/homology
: / IMIDAZOLE / Arachidonate 15-lipoxygenase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsNewie, J. / Neumann, P. / Werner, M. / Mata, R.A. / Ficner, R. / Feussner, I.
CitationJournal: Sci Rep / Year: 2017
Title: Lipoxygenase 2 from Cyanothece sp. controls dioxygen insertion by steric shielding and substrate fixation.
Authors: Newie, J. / Neumann, P. / Werner, M. / Mata, R.A. / Ficner, R. / Feussner, I.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arachidonate 15-lipoxygenase
B: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,37216
Polymers129,0872
Non-polymers1,28514
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-24 kcal/mol
Surface area44440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.710, 167.100, 167.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 41 or resid 43 through 202 or resid 207 through 569))
21(chain B and (resid 1 through 41 or resid 43 through 569))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 1 through 41 or resid 43 through 202 or resid 207 through 569))AA1 - 411 - 41
12LEULEUGLYGLY(chain A and (resid 1 through 41 or resid 43 through 202 or resid 207 through 569))AA43 - 20243 - 202
13ARGARGILEILE(chain A and (resid 1 through 41 or resid 43 through 202 or resid 207 through 569))AA207 - 569207 - 569
21METMETLYSLYS(chain B and (resid 1 through 41 or resid 43 through 569))BB1 - 411 - 41
22LEULEUILEILE(chain B and (resid 1 through 41 or resid 43 through 569))BB43 - 56943 - 569

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Arachidonate 15-lipoxygenase


Mass: 64543.531 Da / Num. of mol.: 2 / Fragment: residues 1-569 / Mutation: L304V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 8801) (bacteria)
Gene: PCC8801_3106 / Plasmid: pET28a / Details (production host): N-terminal His6-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7JX99, arachidonate 15-lipoxygenase

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 15% PEG 4000, 10% Glycerol, 0.1 M MES/immidazol pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→46.35 Å / Num. obs: 53895 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 58.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 22.68
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.60.63.020.859199.9
2.6-2.70.4444.050.913199.7
2.7-2.90.286.120.962199.9
2.9-3.60.09315.740.996199.7
3.6-3.950.0433.360.998199.6
3.95-4.30.03243.440.999199.8
4.3-4.650.02749.380.999199.9
4.65-140.02355.060.999199.6
14-170.0271.381199.4
17-500.01965.050.999195.6
501

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
Cootmodel building
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MED

5med


Resolution: 2.5→46.35 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.33
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2696 5 %Random
Rwork0.1926 ---
obs0.194 53883 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.32 Å2 / Biso mean: 67.0264 Å2 / Biso min: 29.1 Å2
Refinement stepCycle: final / Resolution: 2.5→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9059 0 80 114 9253
Biso mean--87.02 54.88 -
Num. residues----1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079365
X-RAY DIFFRACTIONf_angle_d0.76112745
X-RAY DIFFRACTIONf_chiral_restr0.0421415
X-RAY DIFFRACTIONf_plane_restr0.0051674
X-RAY DIFFRACTIONf_dihedral_angle_d14.4545703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5488X-RAY DIFFRACTION9.296TORSIONAL
12B5488X-RAY DIFFRACTION9.296TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.54550.3581390.284226242763100
2.5455-2.59440.32011410.269226792820100
2.5944-2.64740.30781380.272926252763100
2.6474-2.70490.30811410.264826812822100
2.7049-2.76780.3331390.289726412780100
2.7678-2.8370.33171400.27426552795100
2.837-2.91370.31981400.260626622802100
2.9137-2.99950.2661430.243727032846100
2.9995-3.09630.27791390.23272648278799
3.0963-3.20690.25511410.242726842825100
3.2069-3.33530.30021390.250526442783100
3.3353-3.4870.24531420.240426972839100
3.487-3.67080.25361440.208827232867100
3.6708-3.90070.20511410.183526912832100
3.9007-4.20160.19491430.162727082851100
4.2016-4.62410.1661420.146627052847100
4.6241-5.29240.17211450.142427452890100
5.2924-6.66470.1991460.17627812927100
6.6647-46.35830.16061530.15212891304499
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)
10.3876-0.81450.52850.9074-0.26951.17560.07790.08040.08980.0209-0.17670.15050.02060.2513-0.01240.341-0.0246-0.03560.4060.01850.441412.099316.134829.136
20.17560.0134-0.10480.1098-0.17780.2132-0.22040.01730.039-0.0160.10270.2693-0.1763-0.00100.4745-0.005-0.07450.40830.02840.58589.066334.604829.8039
30.43-0.80040.53271.2593-0.25571.07220.24780.17470.1551-0.1772-0.27750.09970.16850.30820.01560.3870.0999-0.01320.4990.02060.355716.084910.373819.4655
40.2141-0.4380.21780.2869-0.2860.76490.5125-0.00480.2608-0.6921-0.1160.10660.01840.24650.17490.6650.1824-0.2310.4303-0.03940.347725.0143-18.62833.7476
50.0939-0.02940.3290.2828-0.15820.6443-0.0276-0.1086-0.03960.20850.14190.2331-0.02570.0443-00.40620.08030.06770.53010.03920.430728.972-11.829572.6474
60.3755-0.29060.06360.39560.03370.2974-0.1177-0.11880.05790.10050.09410.0355-0.07780.0779-00.45440.0196-0.0080.56870.01320.400835.2861-7.47671.909
70.282-0.5280.92210.8634-0.15351.34050.2773-0.1767-0.1624-0.10250.01240.32030.20150.10590.10250.34410.0127-0.09380.29720.01710.451824.9377-22.333452.1663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 199 )A1 - 199
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 254 )A200 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 569 )A255 - 569
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 70 )B1 - 70
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 172 )B71 - 172
6X-RAY DIFFRACTION6chain 'B' and (resid 173 through 254 )B173 - 254
7X-RAY DIFFRACTION7chain 'B' and (resid 255 through 569 )B255 - 569

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