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- PDB-1ddo: REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP -

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Basic information

Entry
Database: PDB / ID: 1ddo
TitleREDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP
ComponentsD-AMINO ACID OXIDASE
KeywordsFLAVOENZYME / FAD COFACTOR / OXIDOREDUCTASE
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / peroxisomal matrix ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / peroxisomal matrix / digestion / FAD binding / peroxisome / 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
D-TRYPTOPHAN / FLAVIN-ADENINE DINUCLEOTIDE / IMINO-TRYPTOPHAN / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DENSITY AVERAGING / Resolution: 3.1 Å
AuthorsTodone, F. / Mattevi, A.
CitationJournal: Biochemistry / Year: 1997
Title: Active site plasticity in D-amino acid oxidase: a crystallographic analysis.
Authors: Todone, F. / Vanoni, M.A. / Mozzarelli, A. / Bolognesi, M. / Coda, A. / Curti, B. / Mattevi, A.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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
E: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,33326
Polymers315,0228
Non-polymers8,31118
Water1,928107
1
A: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9357
Polymers78,7562
Non-polymers2,1805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-35 kcal/mol
Surface area26580 Å2
MethodPISA
2
B: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9357
Polymers78,7562
Non-polymers2,1805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-35 kcal/mol
Surface area26410 Å2
MethodPISA
3
C: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7316
Polymers78,7562
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-35 kcal/mol
Surface area26380 Å2
MethodPISA
4
D: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7316
Polymers78,7562
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-35 kcal/mol
Surface area26470 Å2
MethodPISA
5
C: D-AMINO ACID OXIDASE
D: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,46212
Polymers157,5114
Non-polymers3,9518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-88 kcal/mol
Surface area50110 Å2
MethodPISA
6
A: D-AMINO ACID OXIDASE
B: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,87114
Polymers157,5114
Non-polymers4,35910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-87 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)325.200, 137.100, 196.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.498937, 0.279368, 0.820375), (0.285444, -0.946772, 0.148808), (0.818281, 0.159926, -0.552123)-11.08144, 21.49235, 13.1464
2given(-0.963292, -0.268456, 0.00031), (-0.26668, 0.956783, -0.115968), (0.030835, -0.111794, -0.993253)162.1611, 28.66857, 105.47461
3given(-0.146425, 0.639987, -0.754306), (-0.055335, 0.756032, 0.652192), (0.987673, 0.137236, -0.075288)178.08078, -0.52553, -53.61571
4given(0.735846, -0.616847, -0.279338), (-0.502688, -0.774007, 0.384991), (-0.453691, -0.142874, -0.879632)117.30955, 89.02817, 110.70526
5given(-0.591486, 0.042068, -0.805217), (-0.027869, -0.999108, -0.031727), (-0.805834, 0.003675, 0.59213)167.03641, 56.1406, 85.6049
6given(-0.541988, -0.729343, 0.417502), (0.686024, -0.670926, -0.281479), (0.485407, 0.133858, 0.86398)183.64554, 27.5622, -63.09723
7given(-0.030669, 0.735246, 0.677106), (-0.142578, 0.667279, -0.731034), (-0.989308, -0.118961, 0.084365)91.93096, 81.46582, 101.65317

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Components

#1: Protein
D-AMINO ACID OXIDASE / / DAAO


Mass: 39377.812 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Organelle: PEROXISOME / References: UniProt: P00371, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ITR / IMINO-TRYPTOPHAN


Mass: 202.209 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H10N2O2
#4: Chemical ChemComp-DTR / D-TRYPTOPHAN / Tryptophan


Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.48 Å3/Da / Density % sol: 60 %
Crystal growpH: 8.3
Details: PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2MM BENZOATE THEN SOAKED IN 20MM D-TRP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 0.6 M / Common name: ammonium succinate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 77977 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.26 Å / Redundancy: 4 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 514100
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
DMmodel building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: DENSITY AVERAGING
Starting model: PDB ENTRY 1KIF

1kif


Resolution: 3.1→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rfree0.25 1000 1.2 %
Rwork0.236 --
all0.236 77977 -
obs0.236 77977 99 %
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21760 0 574 107 22441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.023
X-RAY DIFFRACTIONt_angle_deg3.029
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it6.173
X-RAY DIFFRACTIONt_nbd0.118
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.016

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