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- PDB-3cnp: Crystal structure of fms1 in complex with S-N1-AcMeSpermidine -

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Basic information

Entry
Database: PDB / ID: 3cnp
TitleCrystal structure of fms1 in complex with S-N1-AcMeSpermidine
Componentsfms1
KeywordsOXIDOREDUCTASE / fms1 / N1-acetyl-a-methylspermidine / complex
Function / homology
Function and homology information


non-specific polyamine oxidase / : / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / : / spermine oxidase activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / HDMs demethylate histones / polyamine oxidase activity / spermine catabolic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...non-specific polyamine oxidase / : / N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity / : / spermine oxidase activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / HDMs demethylate histones / polyamine oxidase activity / spermine catabolic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / pantothenate biosynthetic process / Estrogen-dependent gene expression / flavin adenine dinucleotide binding / oxidoreductase activity / chromatin remodeling / chromatin binding / 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 / Chem-SP7 / Polyamine oxidase FMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, Q. / Hao, Q.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of fms1 in complex with S-N1-AcMeSpermidine
Authors: Huang, Q. / Hao, Q.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.3Aug 30, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: fms1
A: fms1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9537
Polymers117,8872
Non-polymers2,0665
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-13 kcal/mol
Surface area37620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.214, 215.201, 117.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein fms1 / Fenpropimorph resistance multicopy suppressor 1


Mass: 58943.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: fms1 / Plasmid: pET28b / 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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SP7 / N-{(1S)-3-[(4-aminobutyl)amino]-1-methylpropyl}acetamide / S-N1-AcMeSpermidine


Mass: 201.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H23N3O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG4000, 0.2M Li2SO4, 0.2M Tris-HCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 3, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 1.95→39.65 Å / Num. all: 94275 / Num. obs: 93521 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.078 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.1 / Num. unique all: 13241 / Rsym value: 0.702 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yy5

1yy5


Resolution: 2.5→31.7 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 4463 -RANDOM
Rwork0.2156 ---
all0.216 45194 --
obs0.216 45014 99.6 %-
Displacement parametersBiso mean: 42.365 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 140 155 8095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.336 756 -
Rwork0.286 --
obs-6732 99.6 %

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