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- PDB-1b5q: A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 1b5q
TitleA 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE
ComponentsPROTEIN (POLYAMINE 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 / N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE / : / Polyamine oxidase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsBinda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase.
Authors: Binda, C. / Coda, A. / Angelini, R. / Federico, R. / Ascenzi, P. / Mattevi, A.
History
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (POLYAMINE OXIDASE)
B: PROTEIN (POLYAMINE OXIDASE)
C: PROTEIN (POLYAMINE OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,77312
Polymers161,0953
Non-polymers4,6779
Water11,313628
1
C: PROTEIN (POLYAMINE OXIDASE)
hetero molecules

C: PROTEIN (POLYAMINE OXIDASE)
hetero molecules

A: PROTEIN (POLYAMINE OXIDASE)
B: PROTEIN (POLYAMINE OXIDASE)
hetero molecules

A: PROTEIN (POLYAMINE OXIDASE)
B: PROTEIN (POLYAMINE OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,54524
Polymers322,1916
Non-polymers9,35418
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation6_654x-y+1,x,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area32310 Å2
ΔGint-19 kcal/mol
Surface area97510 Å2
MethodPISA
2
C: PROTEIN (POLYAMINE OXIDASE)
hetero molecules

C: PROTEIN (POLYAMINE OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1428
Polymers107,3972
Non-polymers3,7456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
MethodPQS
3
A: PROTEIN (POLYAMINE OXIDASE)
B: PROTEIN (POLYAMINE OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2018
Polymers107,3972
Non-polymers2,8056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)184.600, 184.600, 281.500
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(0.137467, 0.494524, -0.858224), (-0.493514, 0.785439, 0.373535), (0.858805, 0.372197, 0.352027)111.852, 50.578, -88.873
2given(-0.391137, -0.363743, 0.845401), (-0.911532, 0.026385, -0.410381), (0.126967, -0.931126, -0.341883)165.979, 148.57001, 64.659

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PROTEIN (POLYAMINE OXIDASE)


Mass: 53698.457 Da / Num. of mol.: 3 / Fragment: FAD-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: GenBank: CAA05249, UniProt: O64411*PLUS

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Sugars , 2 types, 3 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.: 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)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 634 molecules

#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: Chemical ChemComp-MD2 / N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE / MDL72527


Mass: 192.301 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H20N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 293 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlenzyme1drop
2300 mM1dropNaCl
350 mMsodium phosphate1drop
442-48 %satammonium sulfate1reservoir
50.02 %1reservoirNaN3
6100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / 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: 1.9→50 Å / Num. obs: 216570 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Num. obs: 211025 / % possible obs: 96.6 % / Num. measured all: 704940 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
CCP4model building
TNTrefinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.193 211139 -
obs-211139 96 %
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11114 0 317 628 12059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.26
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014
X-RAY DIFFRACTIONt_gen_planes0.018
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 100 Å / σ(F): 0 / Num. reflection Rfree: 2125 / % reflection Rfree: 1 % / Rfactor all: 0.193 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.26
X-RAY DIFFRACTIONt_planar_d0.014
X-RAY DIFFRACTIONt_plane_restr0.018

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