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- PDB-5mef: Cyanothece lipoxygenase 2 (CspLOX2) variant - L304F -

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Basic information

Entry
Database: PDB / ID: 5mef
TitleCyanothece lipoxygenase 2 (CspLOX2) variant - L304F
ComponentsArachidonate 15-lipoxygenase
KeywordsOXIDOREDUCTASE / Linoleate 11-lipoxygenase
Function / homology
Function and homology information


arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / 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: 2.357 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
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

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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)130,11516
Polymers129,1832
Non-polymers93214
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-64 kcal/mol
Surface area44670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 166.260, 166.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Arachidonate 15-lipoxygenase


Mass: 64591.578 Da / Num. of mol.: 2 / Fragment: residues 3- 610 / Mutation: L304F
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, 378 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 15% PEG 4000, 12% glycerol, 0.1 M MES/imidazole 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: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 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: 2.357→46.21 Å / Num. obs: 62963 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 52.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.51
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.357-2.460.5332.70.807199.5
2.46-2.560.3493.750.903198.7
2.56-2.760.2245.970.963199.5
2.76-3.50.07614.380.995199.3
3.5-3.870.03530.290.998199.3
3.87-4.240.02835.980.998198.2
4.24-4.610.02542.290.999199.4
4.61-140.02244.990.999199
14-170.02152.610.999198.7
17-500.02349.880.999195.1
501

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASER2.6phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MED

5med


Resolution: 2.357→46.204 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 3149 5 %Random selection
Rwork0.1907 ---
obs0.192 62942 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 181.07 Å2 / Biso mean: 59.574 Å2 / Biso min: 32.66 Å2
Refinement stepCycle: final / Resolution: 2.357→46.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 54 364 9503
Biso mean--75.2 53.53 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089356
X-RAY DIFFRACTIONf_angle_d0.70712736
X-RAY DIFFRACTIONf_chiral_restr0.0481412
X-RAY DIFFRACTIONf_plane_restr0.0061675
X-RAY DIFFRACTIONf_dihedral_angle_d15.2485694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3571-2.39390.28571420.28072685282799
2.3939-2.43310.30561400.268426612801100
2.4331-2.47510.33131430.27542717286099
2.4751-2.52010.28421390.26722642278199
2.5201-2.56860.31391410.26062678281998
2.5686-2.6210.25821420.25222697283999
2.621-2.6780.29411410.255926842825100
2.678-2.74020.30481430.250127172860100
2.7402-2.80880.29721410.228726792820100
2.8088-2.88470.28021430.23522707285099
2.8847-2.96960.27521410.23282687282899
2.9696-3.06540.24311430.225227132856100
3.0654-3.17490.24331410.22932677281898
3.1749-3.3020.26541420.23512709285199
3.302-3.45230.25551440.21762729287399
3.4523-3.63420.25241450.199827492894100
3.6342-3.86180.20461430.17922711285499
3.8618-4.15980.19811420.16312714285698
4.1598-4.57810.16861450.14462747289299
4.5781-5.23970.16851460.142227672913100
5.2397-6.59840.18121460.17432786293299
6.5984-46.21310.15581560.1572937309398
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)
10.7581-0.50850.61221.609-0.32421.44370.05970.06170.0968-0.0537-0.12290.0678-0.00710.17870.00090.2817-0.0139-0.00150.36790.00820.380712.011215.986628.9416
20.2876-0.28090.1710.4132-0.39650.4969-0.15140.00590.0353-0.065-0.00280.2989-0.20740.0308-0.00070.4512-0.0109-0.05810.39870.01110.50318.886934.3829.7394
30.8852-0.55940.65651.9137-0.15231.74840.19950.26150.1157-0.323-0.2311-0.03510.13080.34850.01610.37880.08670.01280.4570.02710.349615.935510.195119.3273
41.02060.3119-0.69760.22310.03320.94210.64310.4345-0.3002-0.3727-0.28090.01390.01630.0820.98990.99270.2773-0.31570.5788-0.16730.480125.4804-33.740923.9264
50.5044-0.56930.5951.1363-0.52111.14410.0056-0.1592-0.08750.04730.1110.2527-0.11440.029900.33020.00710.03390.43080.00920.421425.2792-7.581857.788
60.7552-0.35130.42890.42090.18660.6953-0.0542-0.07090.09630.28480.1479-0.0285-0.04850.2081-00.5150.07570.02520.5620.00660.464236.974-11.19272.9559
70.4791-0.42510.17350.8467-0.280.549-0.1782-0.2149-0.09540.2810.14710.10870.12130.0437-00.43340.05560.01790.56960.01760.419933.0045-12.08375.2493
81.1496-0.7140.63741.44310.04851.54410.2991-0.0598-0.3217-0.2099-0.00410.23550.45890.23120.08320.5080.0413-0.14440.3598-0.01440.497428.7143-27.708148.481
90.5212-0.80390.0971.4067-0.64091.00120.0171-0.2635-0.1016-0.09520.05360.4918-0.0461-0.2360.00090.3059-0.0138-0.01160.460.06410.472519.0849-14.242257.1326
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 28 )B1 - 28
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 135 )B29 - 135
6X-RAY DIFFRACTION6chain 'B' and (resid 136 through 186 )B136 - 186
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 254 )B187 - 254
8X-RAY DIFFRACTION8chain 'B' and (resid 255 through 445 )B255 - 445
9X-RAY DIFFRACTION9chain 'B' and (resid 446 through 569 )B446 - 569

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