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- PDB-2du8: Crystal structure of human D-amino acid oxidase -

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Basic information

Entry
Database: PDB / ID: 2du8
TitleCrystal structure of human D-amino acid oxidase
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / STRUCTURALLY AMBIVALENT PEPTIDES / CONFORMATIONAL VARIABILITY
Function / homology
Function and homology information


D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / D-serine metabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process ...D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / D-serine metabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / presynaptic active zone / digestion / FAD binding / cell projection / Peroxisomal protein import / extracellular region / identical protein binding / cytosol / cytoplasm
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
BENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKawazoe, T. / Tsuge, H. / Fukui, K.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of human D-amino acid oxidase: Context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring
Authors: Kawazoe, T. / Tsuge, H. / Pilone, M.S. / Fukui, K.
History
DepositionJul 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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

Downloads & links

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Assembly

Deposited unit
A: D-amino-acid oxidase
B: D-amino-acid oxidase
G: D-amino-acid oxidase
J: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,71412
Polymers158,0844
Non-polymers3,6318
Water4,612256
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8576
Polymers79,0422
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-28 kcal/mol
Surface area26890 Å2
MethodPISA
2
G: D-amino-acid oxidase
J: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8576
Polymers79,0422
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-24 kcal/mol
Surface area26980 Å2
MethodPISA
3
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules

G: D-amino-acid oxidase
J: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,71412
Polymers158,0844
Non-polymers3,6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area16510 Å2
ΔGint-67 kcal/mol
Surface area50990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.976, 183.184, 51.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThere are 2 biological units in the asymmetric unit. The biological unit 1 consists of chain(s) A, B. The biological unit 2 consists of chain(s) G, J.

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Components

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


Mass: 39520.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 12% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→116.25 Å / Num. obs: 49644 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.377 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AN9

1an9


Resolution: 2.5→46.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.63 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 1.696 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27006 2516 5.1 %RANDOM
Rwork0.22296 ---
obs0.22535 47032 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.856 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2---1.64 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 248 256 11436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211508
X-RAY DIFFRACTIONr_bond_other_d0.1050.024
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.97115696
X-RAY DIFFRACTIONr_angle_other_deg13.38538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1451356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56423.431548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.464151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7471584
X-RAY DIFFRACTIONr_chiral_restr0.0830.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028892
X-RAY DIFFRACTIONr_gen_planes_other0.0790.024
X-RAY DIFFRACTIONr_nbd_refined0.2220.25217
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27719
X-RAY DIFFRACTIONr_nbtor_other0.290.27
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0521.56919
X-RAY DIFFRACTIONr_mcbond_other0.1361.54
X-RAY DIFFRACTIONr_mcangle_it1.552210920
X-RAY DIFFRACTIONr_scbond_it2.21535628
X-RAY DIFFRACTIONr_scangle_it3.0394.54776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 165 -
Rwork0.284 3310 -
obs--95.23 %

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