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- PDB-3l1r: X-ray structure of the mutant lys300met of polyamine oxidase from... -

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Basic information

Entry
Database: PDB / ID: 3l1r
TitleX-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermidine
ComponentsPolyamine oxidase
KeywordsOXIDOREDUCTASE / Flavoenzyme / Polyamine oxidase / Flavoprotein / Disulfide bond / FAD / Glycoprotein
Function / homology
Function and homology information


polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process / plant-type cell wall ...polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process / plant-type cell wall / apoplast / flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / SPERMIDINE / Polyamine oxidase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFiorillo, A. / Ilari, A. / Tavladoraki, P.
CitationJournal: To be Published
Title: The crystal structure of the mutant k300m of polyamine oxidase from zea mays unveils the role of lys300 in catalysis
Authors: Fiorillo, A. / Ilari, A. / Tavladoraki, P.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyamine oxidase
B: Polyamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69710
Polymers109,0592
Non-polymers2,6398
Water32418
1
A: Polyamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6814
Polymers54,5291
Non-polymers1,1523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0166
Polymers54,5291
Non-polymers1,4875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-10 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.676, 137.676, 189.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyamine oxidase /


Mass: 54529.344 Da / Num. of mol.: 2 / Mutation: K300M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: PAO / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33
References: UniProt: O64411, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor

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Sugars , 2 types, 2 molecules

#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.: 1
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 5 types, 24 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50% SATURATED AMMONIUM SULFATE SOLUTION, 0.1M SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2009
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→46.5 Å / Num. all: 34813 / Num. obs: 34784 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 8.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0043refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KPF

3kpf


Resolution: 3.2→46.5 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.897 / SU B: 13.215 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 1.109 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21627 1749 5 %RANDOM
Rwork0.19247 ---
obs0.19367 32998 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.137 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.77 Å20 Å2
2--1.55 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7487 0 174 18 7679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.97310622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0065931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69623.973375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.128151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4181548
X-RAY DIFFRACTIONr_chiral_restr0.0780.21127
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215945
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3211.54633
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61727475
X-RAY DIFFRACTIONr_scbond_it0.79633183
X-RAY DIFFRACTIONr_scangle_it1.3644.53146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1764medium positional0.190.5
1758loose positional0.295
1764medium thermal0.22
1758loose thermal0.3410
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 136 -
Rwork0.283 2367 -
obs--100 %

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