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- PDB-2e49: Crystal Structure of Human D-Amino Acid Oxidase in Complex with I... -

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Basic information

Entry
Database: PDB / ID: 2.0E+49
TitleCrystal Structure of Human D-Amino Acid Oxidase in Complex with Imino-Serine
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / Structurally ambivalent peptide / Imino-serine 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-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / 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 / presynaptic active zone / peroxisomal matrix / 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
FLAVIN-ADENINE DINUCLEOTIDE / 3-hydroxy-2-iminopropanoic acid / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKawazoe, T. / Tsuge, H. / Imagawa, T. / Fukui, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Structural basis of d-DOPA oxidation by d-amino acid oxidase: Alternative pathway for dopamine biosynthesis.
Authors: Kawazoe, T. / Tsuge, H. / Imagawa, T. / Aki, K. / Kuramitsu, S. / Fukui, K.
History
DepositionDec 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Non-polymer description
Revision 1.4Oct 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
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,63812
Polymers158,0844
Non-polymers3,5558
Water2,018112
1
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8196
Polymers79,0422
Non-polymers1,7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-36 kcal/mol
Surface area27340 Å2
MethodPISA
2
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8196
Polymers79,0422
Non-polymers1,7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-39 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.661, 181.745, 50.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-MH6 / 3-hydroxy-2-iminopropanoic acid


Type: peptide linking / Mass: 103.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 23223 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.223 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DU8

2du8


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.882 / SU B: 22.972 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R Free: 0.648 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 1187 5.1 %RANDOM
Rwork0.22111 ---
all0.22396 ---
obs0.22396 21972 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.757 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å20 Å20 Å2
2---6.9 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 240 112 11284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9715680
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84351356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67823.431548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.143151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0911584
X-RAY DIFFRACTIONr_chiral_restr0.110.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.26175
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.27656
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2507
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.56909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.136210948
X-RAY DIFFRACTIONr_scbond_it1.41335590
X-RAY DIFFRACTIONr_scangle_it1.9214.54732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 80 -
Rwork0.256 1437 -
obs--89.39 %

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