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- PDB-3bi2: Crystal structures of fms1 in complex with its inhibitors -

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Basic information

Entry
Database: PDB / ID: 3bi2
TitleCrystal structures of fms1 in complex with its inhibitors
ComponentsPolyamine oxidase FMS1
KeywordsOXIDOREDUCTASE / enzyme-inhibitor complex / polyamine oxidase
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
dodecane-1,12-diamine / FLAVIN-ADENINE DINUCLEOTIDE / Polyamine oxidase FMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsHuang, Q. / Hao, Q.
CitationJournal: To be Published
Title: Crystal structures of fms1 in complex with its inhibitors
Authors: Huang, Q. / Hao, Q.
History
DepositionNov 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Apr 3, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,8596
Polymers117,8872
Non-polymers1,9724
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.205, 215.323, 116.586
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 Polyamine oxidase FMS1 / E.C.1.5.3.11 / 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: 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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-297 / dodecane-1,12-diamine


Mass: 200.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H28N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 200mM CaCl2, 100mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 57450 / Num. obs: 53831 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.064
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.2 % / Num. unique all: 2857 / Rsym value: 0.246 / % possible all: 86.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native fms1 crystal structure

Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 5068 8.8 %random
Rwork0.222 ---
all-57450 --
obs-53831 93.7 %-
Solvent computationBsol: 38.657 Å2
Displacement parametersBiso mean: 45.948 Å2
Baniso -1Baniso -2Baniso -3
1-9.426 Å20 Å20 Å2
2--18.441 Å20 Å2
3----27.867 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 134 124 7980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d22.72
X-RAY DIFFRACTIONc_improper_angle_d0.862.5
LS refinement shellResolution: 2.3→2.44 Å
RfactorNum. reflection% reflection
Rfree0.355 730 -
Rwork0.321 --
obs-6204 73.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2fad.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4d12.param

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