[English] 日本語
Yorodumi
- PDB-1h83: STRUCTURE OF POLYAMINE OXIDASE IN COMPLEX WITH 1,8-DIAMINOOCTANE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h83
TitleSTRUCTURE OF POLYAMINE OXIDASE IN COMPLEX WITH 1,8-DIAMINOOCTANE
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) / : / : / 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) / : / : / 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 ...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
OCTANE 1,8-DIAMINE / FLAVIN-ADENINE DINUCLEOTIDE / Polyamine oxidase 1
Similarity search - Component
Biological speciesZEA MAYS (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 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 / 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_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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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 / 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLYAMINE OXIDASE
B: POLYAMINE OXIDASE
C: POLYAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,62812
Polymers161,0953
Non-polymers4,5339
Water13,223734
1
A: POLYAMINE OXIDASE
B: POLYAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1058
Polymers107,3972
Non-polymers2,7086
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)111,0468
Polymers107,3972
Non-polymers3,6496
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)184.690, 184.690, 282.220
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(0.137415, -0.486155, 0.863), (0.487254, 0.791736, 0.368424), (-0.86238, 0.369874, 0.345678)85.542, -61.634, 109.364
2given(-0.387211, -0.913086, 0.127832), (-0.357069, 0.020683, -0.933849), (0.850041, -0.407241, -0.334044)192.071, 116.271, -58.239
DetailsIN THE CRYSTAL WHILE THE CHAIN C FORMS A HOMODIMERWITH A SYMMETRY RELATED MOLECULE. THE PROTEIN ISACTIVE AS A MONOMER.

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: 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: UniProt: O64411, EC: 1.5.3.11

-
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

-
Non-polymers , 3 types, 740 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-DIA / OCTANE 1,8-DIAMINE / 1,8-DIAMINOOCTANE / OCTAMETHYLENEDIAMINE / 1,8-OCTANEDIAMINE


Mass: 144.258 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H20N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

-
Details

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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.31 Å3/Da / Density % sol: 71.48 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
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: 215494 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.328 / % possible all: 87.9
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 3.8 % / Num. measured all: 774835
Reflection shell
*PLUS
% possible obs: 87.9 % / Mean I/σ(I) obs: 3.8

-
Processing

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

1b37


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.237 -2 %
Rwork0.196 --
all0.196 215494 -
obs0.196 215494 97.9 %
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11114 0 305 734 12153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.1
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: 2176 / % reflection Rfree: 2 % / Rfactor Rfree: 0.237
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more