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- PDB-5med: Cyanothece lipoxygenase 2 (CspLOX2) -

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Basic information

Entry
Database: PDB / ID: 5med
TitleCyanothece lipoxygenase 2 (CspLOX2)
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
1-BUTANOL / 1,4-BUTANEDIOL / : / HEXANE-1,6-DIOL / 1,3-PROPANDIOL / R-1,2-PROPANEDIOL / N-PROPANOL / Arachidonate 15-lipoxygenase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)130,60121
Polymers129,1152
Non-polymers1,48619
Water18,8441046
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-2 kcal/mol
Surface area44400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 165.400, 166.210
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: 64557.562 Da / Num. of mol.: 2 / Fragment: residues 1-569
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 , 9 types, 1065 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-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#8: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#9: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole, 0.02 M of each alcohol (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2012 / 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: 1.8→45 Å / Num. obs: 134076 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 24.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.8-1.90.5422.060.712176.7
1.9-20.463.190.8199.9
2-2.20.2455.50.928199.9
2.2-3.120.09411.060.988199.4
3.12-3.580.05317.850.992197.3
3.58-4.040.04720.80.992196.7
4.04-4.50.04422.450.993197
4.5-140.03425.730.997197.1
14-170.01928.830.999192.9
17-500.01626.10.999175.9
501

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHASER2.6phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o8y

3o8y


Resolution: 1.8→41.553 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 6700 5 %Random
Rwork0.1735 ---
obs0.1749 133973 95.71 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 114.29 Å2 / Biso mean: 30.3083 Å2 / Biso min: 11.58 Å2
Refinement stepCycle: final / Resolution: 1.8→41.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9061 0 106 1051 10218
Biso mean--45.97 38.18 -
Num. residues----1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089445
X-RAY DIFFRACTIONf_angle_d1.04412837
X-RAY DIFFRACTIONf_chiral_restr0.0661434
X-RAY DIFFRACTIONf_plane_restr0.0081690
X-RAY DIFFRACTIONf_dihedral_angle_d14.1975766
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 (%)
1.8-1.82050.3551700.28123218338872
1.8205-1.84190.29381680.25673191335974
1.8419-1.86430.26931690.24293211338073
1.8643-1.88790.28641760.23683347352376
1.8879-1.91280.28122290.236543354564100
1.9128-1.9390.28212320.237444144646100
1.939-1.96670.2912280.226343374565100
1.9667-1.9960.24912310.219143894620100
1.996-2.02720.25192340.208844354669100
2.0272-2.06050.2532290.19943414570100
2.0605-2.0960.24792340.189244434677100
2.096-2.13410.24022280.186643454573100
2.1341-2.17520.21332330.180944224655100
2.1752-2.21960.22882290.181143524581100
2.2196-2.26780.21492340.182544464680100
2.2678-2.32060.21162290.178243534582100
2.3206-2.37860.20022340.175144254659100
2.3786-2.44290.20722290.170543824611100
2.4429-2.51480.21982320.174244024634100
2.5148-2.59590.20712340.169744414675100
2.5959-2.68870.20222290.16724360458999
2.6887-2.79630.18452320.16664406463899
2.7963-2.92360.19962320.17384399463199
2.9236-3.07760.1982310.16674391462299
3.0776-3.27040.17852290.16644359458898
3.2704-3.52280.21242290.1744352458197
3.5228-3.87710.18712310.1574371460297
3.8771-4.43750.16252300.14674362459297
4.4375-5.58870.16382350.14844464469997
5.5887-41.56360.18012400.16714580482096

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