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- PDB-5fno: Manganese Lipoxygenase -

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Basic information

Entry
Database: PDB / ID: 5fno
TitleManganese Lipoxygenase
ComponentsMANGANESE LIPOXYGENASE
KeywordsOXIDOREDUCTASE / OXIDASE / LIPOXYGENASE / MAGNAPORTHE ORYZAE
Function / homology
Function and homology information


linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / extracellular region / 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 speciesMAGNAPORTHE ORYZAE (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.038 Å
AuthorsWennman, A. / Karkehabadi, S. / Oliw, E.H. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of Manganese Lipoxygenase of the Rice Blast Fungus Magnaporthe Oryzae
Authors: Wennman, A. / Oliw, E.H. / Karkehabadi, S. / Chen, Y.
History
DepositionNov 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE LIPOXYGENASE
B: MANGANESE LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,96310
Polymers134,1192
Non-polymers1,8448
Water12,304683
1
A: MANGANESE LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9815
Polymers67,0601
Non-polymers9224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANGANESE LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9815
Polymers67,0601
Non-polymers9224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.725, 111.374, 171.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MANGANESE LIPOXYGENASE


Mass: 67059.578 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNAPORTHE ORYZAE (rice blast fungus) / Strain: GUY11 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X11 / References: UniProt: G4NAP4, linoleate 11-lipoxygenase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.2M AMMONIUM CITRATE DIBASIC 12% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.77
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.07→29.7 Å / Num. obs: 81415 / % possible obs: 98.1 % / Observed criterion σ(I): 2.7 / Redundancy: 18.8 % / Biso Wilson estimate: 35.86 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.9
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.9 / % possible all: 86

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.038→29.705 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 4185 5 %
Rwork0.1679 --
obs0.1701 84176 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.8 Å2
Refinement stepCycle: LAST / Resolution: 2.038→29.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 114 683 9741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079291
X-RAY DIFFRACTIONf_angle_d0.92112666
X-RAY DIFFRACTIONf_dihedral_angle_d12.4855508
X-RAY DIFFRACTIONf_chiral_restr0.0511406
X-RAY DIFFRACTIONf_plane_restr0.0061662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0384-2.06150.25141000.21561956X-RAY DIFFRACTION72
2.0615-2.08580.29321210.20622214X-RAY DIFFRACTION82
2.0858-2.11120.24111220.1942373X-RAY DIFFRACTION88
2.1112-2.13790.22581350.19572535X-RAY DIFFRACTION93
2.1379-2.1660.23971480.1812559X-RAY DIFFRACTION95
2.166-2.19570.24491370.18972656X-RAY DIFFRACTION97
2.1957-2.22710.23211250.18952659X-RAY DIFFRACTION97
2.2271-2.26030.31671390.26182604X-RAY DIFFRACTION96
2.2603-2.29560.23141330.20642682X-RAY DIFFRACTION98
2.2956-2.33320.24051370.18292655X-RAY DIFFRACTION98
2.3332-2.37340.28791280.17852722X-RAY DIFFRACTION98
2.3734-2.41660.21211410.17622653X-RAY DIFFRACTION98
2.4166-2.4630.22561260.182730X-RAY DIFFRACTION99
2.463-2.51330.23491300.17892702X-RAY DIFFRACTION99
2.5133-2.56790.2351660.17812671X-RAY DIFFRACTION99
2.5679-2.62760.24491320.17892749X-RAY DIFFRACTION99
2.6276-2.69330.23481540.17882696X-RAY DIFFRACTION99
2.6933-2.7660.22711390.17632723X-RAY DIFFRACTION99
2.766-2.84740.23971570.1822728X-RAY DIFFRACTION100
2.8474-2.93920.25541690.18182700X-RAY DIFFRACTION99
2.9392-3.04410.21811460.1852733X-RAY DIFFRACTION100
3.0441-3.16590.23271270.18292761X-RAY DIFFRACTION100
3.1659-3.30980.19241500.17452756X-RAY DIFFRACTION100
3.3098-3.48410.21721150.172803X-RAY DIFFRACTION100
3.4841-3.7020.21521360.16392786X-RAY DIFFRACTION100
3.702-3.98720.19851560.15062780X-RAY DIFFRACTION100
3.9872-4.38730.17461540.13352783X-RAY DIFFRACTION100
4.3873-5.01950.17591590.1312802X-RAY DIFFRACTION100
5.0195-6.3140.21181330.16732864X-RAY DIFFRACTION100
6.314-29.70850.18781700.16172956X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.1556 Å / Origin y: 52.3502 Å / Origin z: 93.5407 Å
111213212223313233
T0.2251 Å20.0018 Å2-0.0507 Å2-0.2032 Å20.0001 Å2--0.2858 Å2
L0.84 °2-0.0184 °2-0.2932 °2-0.4754 °20.235 °2--1.1541 °2
S-0.0733 Å °-0.0416 Å °0.2171 Å °0.0447 Å °0.0848 Å °0.0067 Å °-0.1597 Å °0.0917 Å °-0.0035 Å °
Refinement TLS groupSelection details: ALL

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