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- PDB-1kif: D-AMINO ACID OXIDASE FROM PIG KIDNEY -

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Basic information

Entry
Database: PDB / ID: 1kif
TitleD-AMINO ACID OXIDASE FROM PIG KIDNEY
ComponentsD-AMINO ACID OXIDASE
KeywordsFLAVOPROTEIN / FAD COFACTOR / OXIDASE / FLAVOENZYME
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-amino acid catabolic process / D-serine catabolic process / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium ...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-amino acid catabolic process / D-serine catabolic process / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / presynaptic active zone / peroxisomal matrix / digestion / FAD binding / cell projection / peroxisome / extracellular region / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsTodone, F. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
Authors: Mattevi, A. / Vanoni, M.A. / Todone, F. / Rizzi, M. / Teplyakov, A. / Coda, A. / Bolognesi, M. / Curti, B.
History
DepositionJan 19, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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)322,28424
Polymers315,0228
Non-polymers7,26116
Water5,296294
1
A: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5716
Polymers78,7562
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-25 kcal/mol
Surface area26680 Å2
MethodPISA
2
B: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5716
Polymers78,7562
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-25 kcal/mol
Surface area26610 Å2
MethodPISA
3
C: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5716
Polymers78,7562
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-25 kcal/mol
Surface area26560 Å2
MethodPISA
4
D: D-AMINO ACID OXIDASE
H: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5716
Polymers78,7562
Non-polymers1,8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-25 kcal/mol
Surface area26560 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)161,14212
Polymers157,5114
Non-polymers3,6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16450 Å2
ΔGint-68 kcal/mol
Surface area50080 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)161,14212
Polymers157,5114
Non-polymers3,6318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-67 kcal/mol
Surface area50310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)326.480, 138.100, 200.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTALS CONTAINS 8 ENZYME SUBUNITS. WITH THE EXCEPTION OF 16 SIDE CHAINS, THE 8 SUBUNITS WERE KEPT IDENTICAL DURING REFINEMENT BY IMPOSING A NON-CRYSTALLOGRAPHIC-SYMMETRY CONSTRAINT. THE FOLLOWING RESIDUES WERE NOT NCS CONSTRAINED: HIS 24, GLN 28, PRO 29, GLU 58, PRO 59, SER 60, ASN 61, ASN 66, ASP 127, ARG 129, ARG 162, GLU 165, ASN 248, ILE 253, ARG 265, ARG 337.

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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 / Details: OXIDIZED STATE / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Organelle: PEROXISOME / References: UniProt: P00371, D-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 122.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Details: 293K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 28 ℃ / Method: vapor diffusion / pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
22 mMsodium benzoate1drop
30.5 Mammonium succinate1reservoir
4100 mMTris-HCl1reservoirpH8.3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 119327 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.6→2.8 Å / % possible all: 45.2
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 592028

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 2.6→20 Å / Num. reflection Rfree: 1000 / Num. reflection obs: 119237 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21760 0 496 294 22550
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0170.2
X-RAY DIFFRACTIONt_angle_deg2.83
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0070.02
X-RAY DIFFRACTIONt_it4.6
X-RAY DIFFRACTIONt_nbd0.052
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.228 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.2
X-RAY DIFFRACTIONt_angle_deg32.8

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