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- PDB-1h81: STRUCTURE OF POLYAMINE OXIDASE IN THE REDUCED STATE -

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Basic information

Entry
Database: PDB / ID: 1h81
TitleSTRUCTURE OF POLYAMINE OXIDASE IN THE REDUCED STATE
ComponentsPOLYAMINE OXIDASE
KeywordsOXIDOREDUCTASE / FLAVIN-DEPENDENT AMINE OXIDASE
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 / Polyamine oxidase 1
Similarity search - Component
Biological speciesZEA MAYS (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBinda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A.
CitationJournal: Biochemistry / Year: 2001
Title: Structural Bases for Inhibitor Binding and Catalysis in Polyamine Oxidase
Authors: Binda, C. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A.
History
DepositionJan 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_close_contact / 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_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
C: POLYAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1969
Polymers161,0953
Non-polymers4,1006
Water13,043724
1
A: POLYAMINE OXIDASE
B: POLYAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8176
Polymers107,3972
Non-polymers2,4204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: POLYAMINE OXIDASE
hetero molecules

C: POLYAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7586
Polymers107,3972
Non-polymers3,3614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)181.770, 181.770, 277.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.137894, -0.485816, 0.863115), (0.487082, 0.792042, 0.367994), (-0.862402, 0.369664, 0.34585)84.164, -60.693, 107.706
2given(-0.387625, -0.912764, 0.128873), (-0.357429, 0.019957, -0.933727), (0.849701, -0.407999, -0.333984)189.078, 114.484, -57.267
DetailsIN THE CRYSTAL WHILE THE CHAIN C FORMS A HOMODIMERWITH A SYMMETRY RELATED MOLECULE. THE PROTEIN ISACTIVE AS A MONOMER.

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Components

#1: Protein POLYAMINE OXIDASE /


Mass: 53698.457 Da / Num. of mol.: 3 / Fragment: FAD-BINDING DOMAIN RESIDUES 29-500 / Source method: isolated from a natural source / Source: (natural) ZEA MAYS (maize) / References: UniProt: O64411, EC: 1.5.3.11
#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: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4[DFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3/a3-b1_a4-c1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE OXIDATION OF THE SECONDARY AMINO GROUP OF POLYAMINES (SPERMINE, SPERMIDINE AND THEIR ...CATALYSES THE OXIDATION OF THE SECONDARY AMINO GROUP OF POLYAMINES (SPERMINE, SPERMIDINE AND THEIR ACETYL DERIVATIVES) THIS IS IMPORTANT FOR REGULATION OF POLYAMINE INTRACELLULAR CONCENTRATION.

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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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlenzyme1drop
2300 mM1dropNaCl
350 mMsodium phosphate1drop
442-50 %satammonium sulfate1reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 156868 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.176 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 1527497 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 10.3

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Processing

Software
NameVersionClassification
TNT5Drefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B37

1b37


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.235 -2 %
Rwork0.191 --
all0.191 156392 -
obs0.191 156392 99.1 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11114 0 275 724 12113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 1570 / % reflection Rfree: 2 % / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.013
X-RAY DIFFRACTIONt_plane_restr0.015

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