[English] 日本語
Yorodumi
- PDB-5lae: Crystal structure of murine N1-acetylpolyamine oxidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lae
TitleCrystal structure of murine N1-acetylpolyamine oxidase
ComponentsPeroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
KeywordsOXIDOREDUCTASE / flavin amine oxidase
Function / homology
Function and homology information


N1-acetylpolyamine oxidase / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / putrescine catabolic process / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process ...N1-acetylpolyamine oxidase / PAOs oxidise polyamines to amines / positive regulation of spermidine biosynthetic process / Interconversion of polyamines / putrescine biosynthetic process / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / putrescine catabolic process / polyamine oxidase activity / polyamine catabolic process / spermine catabolic process / spermidine catabolic process / Peroxisomal protein import / peroxisomal matrix
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSjogren, T. / Aagaard, A. / Snijder, A. / Barlind, L.
CitationJournal: Biochemistry / Year: 2017
Title: The Structure of Murine N(1)-Acetylspermine Oxidase Reveals Molecular Details of Vertebrate Polyamine Catabolism.
Authors: Sjogren, T. / Wassvik, C.M. / Snijder, A. / Aagaard, A. / Kumanomidou, T. / Barlind, L. / Kaminski, T.P. / Kashima, A. / Yokota, T. / Fjellstrom, O.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6044
Polymers54,6351
Non-polymers9703
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.975, 121.975, 55.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Peroxisomal N(1)-acetyl-spermine/spermidine oxidase,Peroxisomal N(1)-acetyl-spermine/spermidine oxidase / Polyamine oxidase


Mass: 54634.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence includes 3 aa N-terminal deletion and a loop deletion where 6 residues (451-457) are replaced with a single glycine residue.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Paox, Pao / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8C0L6, N1-acetylpolyamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 23mg/ml in 20 mM HEPES, pH 7.0, 100 mM NaCl, 5% (v/v) glycerol and 2.5 mM TCEP was equilibrated against 2.2 M (NH4)2SO4, 0.2 M NaSCN, 0.1 M Tris pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2015
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.85→49 Å / Num. obs: 40245 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 26.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 95

-
Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQ5

1bq5


Resolution: 1.85→49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2038 5.08 %RANDOM
Rwork0.179 ---
obs0.181 40091 100 %-
Displacement parametersBiso mean: 31.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.6123 Å20 Å20 Å2
2--0.6123 Å20 Å2
3----1.2246 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 65 287 3886
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093687HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965011HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1248SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes572HARMONIC5
X-RAY DIFFRACTIONt_it3687HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion16.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
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_contact4468SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 149 5.08 %
Rwork0.21 2782 -
all0.212 2931 -
obs--100 %

+
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