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- PDB-1z6l: crystal structure of Fms1 in complex with its substrate -

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Basic information

Entry
Database: PDB / ID: 1z6l
Titlecrystal structure of Fms1 in complex with its substrate
ComponentsPolyamine oxidase FMS1
KeywordsOXIDOREDUCTASE / Fms1 / bis(hexamethylene)triamine / 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
N-(6-AMINOHEXYL)HEXANE-1,6-DIAMINE / FLAVIN-ADENINE DINUCLEOTIDE / Polyamine oxidase FMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, Q. / Liu, Q. / Hao, Q.
Citation
Journal: To be Published
Title: crystal structure of Fms1 in complex with its substrate
Authors: Huang, Q. / Liu, Q. / Hao, Q.
#1: Journal: To be Published
Title: crystal structure of Fms1 and its complex with spermine reveal substrate specificity
Authors: Huang, Q. / Liu, Q. / Hao, Q.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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)119,8896
Polymers117,8872
Non-polymers2,0024
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-29 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.038, 214.616, 118.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Polyamine oxidase 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 / Production host: Escherichia coli (E. coli) / 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-DRE / N-(6-AMINOHEXYL)HEXANE-1,6-DIAMINE / BIS(HEXAMETHYLENE)TRIAMINE


Mass: 215.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H29N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.956 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, Hepes, CaCL2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2004 / Details: SILICON
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 43047 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 73.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native Fms1

Resolution: 2.5→41.71 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3 4161 RANDOM
Rwork0.237 --
all0.237 45530 -
obs0.3 41023 -
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7786 0 136 130 8052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.5→2.66 Å
RfactorNum. reflection
Rfree0.423 594
Rwork0.374 -
obs-4787

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