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- PDB-4gdp: Yeast polyamine oxidase FMS1, N195A mutant -

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Basic information

Entry
Database: PDB / ID: 4gdp
TitleYeast polyamine oxidase FMS1, N195A mutant
ComponentsPolyamine oxidase FMS1
KeywordsOXIDOREDUCTASE / FAD cofactor / oxidase / flavoenzyme / mutant
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 / MOLECULAR REPLACEMENT / Resolution: 1.9998 Å
AuthorsTaylor, A.B. / Adachi, M.S. / Hart, P.J. / Fitzpatrick, P.F.
CitationJournal: Biochemistry / Year: 2012
Title: Mechanistic and Structural Analyses of the Roles of Active Site Residues in Yeast Polyamine Oxidase Fms1: Characterization of the N195A and D94N Enzymes.
Authors: Adachi, M.S. / Taylor, A.B. / Hart, P.J. / Fitzpatrick, P.F.
History
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyamine oxidase FMS1
B: Polyamine oxidase FMS1
C: Polyamine oxidase FMS1
D: Polyamine oxidase FMS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,52112
Polymers235,6024
Non-polymers3,9198
Water13,025723
1
A: Polyamine oxidase FMS1
B: Polyamine oxidase FMS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7616
Polymers117,8012
Non-polymers1,9604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-14 kcal/mol
Surface area38820 Å2
MethodPISA
2
C: Polyamine oxidase FMS1
D: Polyamine oxidase FMS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7616
Polymers117,8012
Non-polymers1,9604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-12 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.851, 81.885, 104.791
Angle α, β, γ (deg.)78.07, 79.51, 78.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Polyamine oxidase FMS1 / Fenpropimorph resistance multicopy suppressor 1


Mass: 58900.570 Da / Num. of mol.: 4 / Mutation: N195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FMS1, YM9711.09, YMR020W / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50264, non-specific polyamine oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Di-Ethyleneglycol, Tri-Ethyleneglycol, Tetra-Ethyleneglycol, Penta-Ethyleneglycol, 0.1M Imidazole; MES, 30% Ethylene glycol, PEG 8000 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9998→100 Å / Num. obs: 149689 / % possible obs: 89 % / Redundancy: 3.4 % / Rsym value: 0.109 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9998→2.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.408 / % possible all: 75.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ECH

4ech


Resolution: 1.9998→79.074 Å / SU ML: 0.24 / Isotropic thermal model: isotropic / σ(F): 1.44 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1999 1.34 %
Rwork0.2025 --
obs0.203 149579 88.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.54 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.1052 Å29.3533 Å215.042 Å2
2---1.611 Å29.9853 Å2
3----2.7714 Å2
Refinement stepCycle: LAST / Resolution: 1.9998→79.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15869 0 260 723 16852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416512
X-RAY DIFFRACTIONf_angle_d0.87522358
X-RAY DIFFRACTIONf_dihedral_angle_d14.4626158
X-RAY DIFFRACTIONf_chiral_restr0.0672445
X-RAY DIFFRACTIONf_plane_restr0.0032890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9998-2.04980.32831190.25838788X-RAY DIFFRACTION74
2.0498-2.10520.26691280.24979464X-RAY DIFFRACTION80
2.1052-2.16720.32451370.236210084X-RAY DIFFRACTION85
2.1672-2.23710.2651430.231110535X-RAY DIFFRACTION89
2.2371-2.31710.28811390.221810269X-RAY DIFFRACTION87
2.3171-2.40990.27141510.21311164X-RAY DIFFRACTION94
2.4099-2.51950.23641510.204711108X-RAY DIFFRACTION94
2.5195-2.65240.23821490.20711012X-RAY DIFFRACTION93
2.6524-2.81860.2921430.207710487X-RAY DIFFRACTION88
2.8186-3.03620.27031510.212411182X-RAY DIFFRACTION94
3.0362-3.34180.23471480.201711012X-RAY DIFFRACTION93
3.3418-3.82530.20871430.185310553X-RAY DIFFRACTION89
3.8253-4.81940.16981510.167811168X-RAY DIFFRACTION94
4.8194-79.13620.21911460.207110754X-RAY DIFFRACTION91

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