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- PDB-3w4i: Crystal Structure of human DAAO in complex with coumpound 8 -

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Basic information

Entry
Database: PDB / ID: 3w4i
TitleCrystal Structure of human DAAO in complex with coumpound 8
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE
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
pyridine-2,3-diol / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Revision 1.2Mar 20, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: 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)161,67012
Polymers158,0844
Non-polymers3,5878
Water00
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8356
Polymers79,0422
Non-polymers1,7934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-41 kcal/mol
Surface area26510 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8356
Polymers79,0422
Non-polymers1,7934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-39 kcal/mol
Surface area26540 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15270 Å2
ΔGint-97 kcal/mol
Surface area50130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.696, 181.529, 50.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 1 - 340 / Label seq-ID: 1 - 340

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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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-8LG / pyridine-2,3-diol


Mass: 111.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5NO2

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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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 8
Details: 10-15% (w/v) PEG 4000, 0.1M sodium citrate pH8.0, 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: 2.5→115.03 Å / Num. all: 46531 / Num. obs: 46531 / % possible obs: 96.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.595.10.423189.8
2.59-2.695.20.314191.9
2.69-2.825.30.213193.8
2.82-2.965.40.146195.4
2.96-3.155.50.099196.6
3.15-3.395.60.064197.8
3.39-3.735.80.041198.4
3.73-4.275.90.026198.8
4.27-5.3860.022199.6
5.38-505.70.021198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.794 / SU ML: 0.284 / SU R Cruickshank DPI: 0.2993 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27285 2350 5.1 %RANDOM
Rwork0.23568 ---
obs0.23754 44130 96.02 %-
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 mean: 55.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 244 0 11176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02111504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.97115692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73151356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12223.431548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.378151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6591584
X-RAY DIFFRACTIONr_chiral_restr0.0950.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.56752
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.379210920
X-RAY DIFFRACTIONr_scbond_it1.40934752
X-RAY DIFFRACTIONr_scangle_it2.2964.54772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2794 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.190.05
Btight positional0.190.05
Ctight positional0.180.05
Dtight positional0.190.05
Atight thermal2.050.5
Btight thermal1.530.5
Ctight thermal1.830.5
Dtight thermal1.980.5
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 166 -
Rwork0.331 2959 -
obs--88.75 %

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