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- PDB-1dao: COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-ME... -

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Basic information

Entry
Database: PDB / ID: 1dao
TitleCOVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID
ComponentsD-AMINO ACID OXIDASE
KeywordsFLAVOENZYME / FAD COFACTOR / OXIDOREDUCTASE
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / presynaptic active zone / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / cell projection / peroxisome / extracellular region / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / 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 oxidases signature. / D-amino-acid oxidase / 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-N5-ISOBUTYL KETONE / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DENSITY AVERAGING / Resolution: 3.2 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)321,86816
Polymers315,0228
Non-polymers6,8458
Water1448
1
A: D-AMINO ACID OXIDASE
E: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4674
Polymers78,7562
Non-polymers1,7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-31 kcal/mol
Surface area26340 Å2
MethodPISA
2
B: D-AMINO ACID OXIDASE
F: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4674
Polymers78,7562
Non-polymers1,7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-30 kcal/mol
Surface area26330 Å2
MethodPISA
3
C: D-AMINO ACID OXIDASE
G: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4674
Polymers78,7562
Non-polymers1,7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-30 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)80,4674
Polymers78,7562
Non-polymers1,7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-31 kcal/mol
Surface area26290 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)160,9348
Polymers157,5114
Non-polymers3,4234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-77 kcal/mol
Surface area49960 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)160,9348
Polymers157,5114
Non-polymers3,4234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-76 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)326.400, 136.900, 196.500
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(-0.570354, 0.003517, -0.821391), (0.014255, -0.999798, -0.014179), (-0.821275, -0.019797, 0.570189)168.05963, 52.36601, 88.35892
2given(-0.512203, -0.770115, 0.380225), (0.71598, -0.627382, -0.30621), (0.474363, 0.115392, 0.872734)184.94926, 25.59378, -63.19735
3given(-0.029573, 0.755763, 0.654177), (-0.145143, 0.64428, -0.750891), (-0.988969, -0.117155, 0.090641)92.51457, 83.21375, 101.60513
4given(0.492259, 0.293836, 0.819355), (0.285852, -0.943666, 0.16668), (0.822174, 0.152165, -0.548522)-10.75768, 19.98264, 12.50754
5given(-0.951879, -0.305549, -0.023776), (-0.298626, 0.942156, -0.152198), (0.068905, -0.137774, -0.988064)164.37463, 32.72658, 103.59933
6given(-0.130023, 0.640602, -0.756785), (-0.076196, 0.754551, 0.651802), (0.988579, 0.142413, -0.049298)177.94754, -0.12264, -55.1994
7given(0.718373, -0.618731, -0.317981), (-0.499181, -0.776839, 0.383848), (-0.484519, -0.117016, -0.866919)120.8435, 89.04542, 112.54649

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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-FAB / FLAVIN-ADENINE DINUCLEOTIDE-N5-ISOBUTYL KETONE


Mass: 855.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H39N9O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 72287 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 433795
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

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

1kif


Resolution: 3.2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT
Details: THE 8 SUBUNITS WERE KEPT IDENTICAL EXCEPT FOR RESIDUES 56 - 65, 125 - 130, 157 - 180, 254, 265, 270, 288, THAT WERE RESTRAINED.
RfactorNum. reflection% reflection
Rfree0.26 1000 -
Rwork0.232 --
all0.232 72287 -
obs0.232 72287 99 %
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21760 0 464 8 22232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3.35
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it7.103
X-RAY DIFFRACTIONt_nbd0.12
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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