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- PDB-5fx8: Complete structure of manganese lipoxygenase of Gaeumannomyces gr... -

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Basic information

Entry
Database: PDB / ID: 5fx8
TitleComplete structure of manganese lipoxygenase of Gaeumannomyces graminis and partial structure of zonadhesin of Komagataella pastoris
Components
  • LINOLEATE 11-LIPOXYGENASE
  • ZONADHESIN
KeywordsOXIDOREDUCTASE / CHIAN A AND B / LINOLEATE 11S-AND 13R- LIPOXYGENASE / FATTTY ACID OXYGENATION / MANGANESE. CHAIN U / FUNGAL ADHESION PROTEIN N-TERMINAL DOMAIN
Function / homology
Function and homology information


linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / : / cell wall / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
triacetyl-beta-chitotriose / : / Putative adhesin / Manganese lipoxygenase
Similarity search - Component
Biological speciesGAEUMANNOMYCES GRAMINIS (fungus)
KOMAGATAELLA PHAFFII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y. / Wennman, A. / Karkehanadi, S. / Engstrom, A. / Oliw, E.H.
CitationJournal: J.Lipid Res. / Year: 2016
Title: Crystal Structure of Linoleate 13R-Manganese Lipoxygenase and an Adhesion Protein
Authors: Chen, Y. / Wennman, A. / Karkehabadi, S. / Engstrom, A. / Oliw, E.H.
History
DepositionFeb 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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.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
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LINOLEATE 11-LIPOXYGENASE
B: LINOLEATE 11-LIPOXYGENASE
U: ZONADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,42015
Polymers169,8793
Non-polymers3,54112
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)226.309, 50.470, 177.622
Angle α, β, γ (deg.)90.00, 91.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 3 molecules ABU

#1: Protein LINOLEATE 11-LIPOXYGENASE / LINOLEATE 13S-LIPOXYGENASE / LINOLEATE DIOXYGENASE / MANGANESE LIPOXYGENASE / 13R-LIPOXYGENASE


Mass: 67658.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GAEUMANNOMYCES GRAMINIS (fungus) / Strain: VAR. AVENAE / Description: CBS 870.03 / Plasmid: PPICZALPHA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X11 / References: UniProt: Q8X151, linoleate 13S-lipoxygenase
#2: Protein ZONADHESIN


Mass: 34562.527 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Source method: isolated from a natural source / Details: RESIDUE 20-339 / Source: (natural) KOMAGATAELLA PHAFFII (fungus) / Strain: CBS 7435 / References: UniProt: F2QXM5

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Sugars , 4 types, 10 molecules

#3: 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.: 3
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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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

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Non-polymers , 2 types, 225 molecules

#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 0.1M MES-IMIDAZOLE PH6.5, 20%(V/V) GLYCEROL, 10%(W/V)PEG4000, 0.03M MAGNESIUM CHLORIDE, 0.03M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→49.4 Å / Num. obs: 62790 / % possible obs: 97.8 % / Observed criterion σ(I): 2.4 / Redundancy: 2.9 % / Biso Wilson estimate: 27.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FNO

5fno


Resolution: 2.6→43.163 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 3049 5.1 %
Rwork0.1952 --
obs0.1977 60262 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11094 0 226 223 11543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311620
X-RAY DIFFRACTIONf_angle_d1.15215841
X-RAY DIFFRACTIONf_dihedral_angle_d14.1736783
X-RAY DIFFRACTIONf_chiral_restr0.0661769
X-RAY DIFFRACTIONf_plane_restr0.0072072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64070.34131340.24862636X-RAY DIFFRACTION96
2.6407-2.6840.32411520.24992571X-RAY DIFFRACTION97
2.684-2.73020.28891400.24922524X-RAY DIFFRACTION95
2.7302-2.77990.28571360.242619X-RAY DIFFRACTION97
2.7799-2.83330.31611420.25132619X-RAY DIFFRACTION97
2.8333-2.89110.29311230.23692588X-RAY DIFFRACTION98
2.8911-2.9540.29881360.23542637X-RAY DIFFRACTION97
2.954-3.02270.25321670.23722557X-RAY DIFFRACTION97
3.0227-3.09830.30411350.2322603X-RAY DIFFRACTION97
3.0983-3.1820.3021850.21852590X-RAY DIFFRACTION97
3.182-3.27560.30931090.22032567X-RAY DIFFRACTION96
3.2756-3.38130.23681430.21242574X-RAY DIFFRACTION94
3.3813-3.50210.28271280.20232620X-RAY DIFFRACTION98
3.5021-3.64230.26371350.18572641X-RAY DIFFRACTION97
3.6423-3.80790.22271540.18722566X-RAY DIFFRACTION96
3.8079-4.00860.19981270.17092622X-RAY DIFFRACTION96
4.0086-4.25950.20031110.15652634X-RAY DIFFRACTION95
4.2595-4.5880.17721400.14882578X-RAY DIFFRACTION95
4.588-5.04910.18841340.15232642X-RAY DIFFRACTION96
5.0491-5.77830.18931440.16882569X-RAY DIFFRACTION95
5.7783-7.27430.25631300.19492597X-RAY DIFFRACTION93
7.2743-43.16940.20191440.16422659X-RAY DIFFRACTION93

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