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- PDB-3w4j: Crystal Structure of human DAAO in complex with coumpound 12 -

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Basic information

Entry
Database: PDB / ID: 3w4j
TitleCrystal Structure of human DAAO in complex with coumpound 12
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / Peroxisomal protein import / identical protein binding / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsHondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. ...Hondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. / Orita, M. / Watanabe, T. / Takeuchi, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: 4-Hydroxypyridazin-3(2H)-one Derivatives as Novel d-Amino Acid Oxidase Inhibitors.
Authors: Hondo, T. / Warizaya, M. / Niimi, T. / Namatame, I. / Yamaguchi, T. / Nakanishi, K. / Hamajima, T. / Harada, K. / Sakashita, H. / Matsumoto, Y. / Orita, M. / Takeuchi, M.
History
DepositionJan 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: D-amino-acid oxidase
B: D-amino-acid oxidase
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,08712
Polymers158,0844
Non-polymers4,0038
Water00
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0436
Polymers79,0422
Non-polymers2,0024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-42 kcal/mol
Surface area26310 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0436
Polymers79,0422
Non-polymers2,0024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-39 kcal/mol
Surface area26510 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-97 kcal/mol
Surface area50040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.249, 182.325, 50.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
D-amino-acid oxidase / DAAO / DAMOX / DAO


Mass: 39520.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14920, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-2LD / 3-hydroxy-5-(2-phenylethyl)pyridin-2(1H)-one


Mass: 215.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H13NO2

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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: 2.18 Å3/Da / Density % sol: 43.6 % / Mosaicity: 0.439 °
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 8
Details: 10-15% (w/v) PEG 4000, 0.1M sodium citrate pH 8.0, 0.2M ammonium dihydrogen phosphate, 10% (v/v) glycerol, sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 22, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→115.49 Å / Num. obs: 36583 / % possible obs: 97.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Χ2: 0.85 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.74-2.845.10.42834950.871194.4
2.84-2.955.20.32935070.91195.5
2.95-3.095.20.23235690.914197
3.09-3.255.30.17635770.933197
3.25-3.455.40.11136450.957198.1
3.45-3.725.60.0736620.914198.4
3.72-4.095.60.04436650.872198.5
4.09-4.685.60.02937460.77199.2
4.68-5.95.70.02537800.717199.3
5.9-505.40.01939370.678197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2699 / WRfactor Rwork: 0.1972 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7436 / SU B: 0.004 / SU ML: 0 / SU R Cruickshank DPI: 0.3359 / SU Rfree: 0.4626 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 1826 5 %RANDOM
Rwork0.2104 ---
obs0.2144 36538 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 105.61 Å2 / Biso mean: 55.0209 Å2 / Biso min: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---2.04 Å20 Å2
3---2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 276 0 11208
LS refinement shellResolution: 2.738→2.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 137 -
Rwork0.246 2441 -
all-2578 -
obs--93.54 %

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