[English] 日本語
Yorodumi
- PDB-1rsg: Crystal structure of the polyamine oxidase Fms1 from yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rsg
TitleCrystal structure of the polyamine oxidase Fms1 from yeast
ComponentsFMS1 protein
KeywordsOXIDOREDUCTASE / FAD binding motif
Function / homology
Function and homology information


non-specific polyamine oxidase / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / pantothenate biosynthetic process / flavin adenine dinucleotide binding ...non-specific polyamine oxidase / spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity / N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity / spermine:oxygen oxidoreductase (spermidine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / pantothenate biosynthetic process / flavin adenine dinucleotide binding / oxidoreductase activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / cytoplasm
Similarity search - Function
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 FMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHuang, Q. / Liu, Q. / Hao, Q.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of fms1 and its complex with spermine reveal substrate specificity.
Authors: Huang, Q. / Liu, Q. / Hao, Q.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Yeast Fms1 is a FAD-utilizing polyamine oxidase
Authors: Landry, J. / Sternglanz, R.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMS1 protein
B: FMS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5844
Polymers119,0132
Non-polymers1,5712
Water17,457969
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-31 kcal/mol
Surface area39350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.385, 103.126, 77.590
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2162-

HOH

-
Components

#1: Protein FMS1 protein


Mass: 59506.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FMS1, YMR020W, YM9711.09 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50264, EC: 1.5.3.11
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.979106
SYNCHROTRONCHESS F220.963882
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 31, 2003
RadiationMonochromator: GRAPHITE / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791061
20.9638821
ReflectionResolution: 1.9→40 Å / Num. all: 100168 / Num. obs: 96862 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.302 / Num. unique all: 3607 / % possible all: 73

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SAPImodel building
ABSmodel building
CNSrefinement
SAPIphasing
ABSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.95 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 9391 -RANDOM
Rwork0.206 ---
all0.21 100168 --
obs0.21 93744 93.4 %-
Displacement parametersBiso mean: 35.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7786 0 106 969 8861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.303 1265 -
Rwork0.266 --
obs-12487 75.2 %

+
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