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- PDB-1an9: D-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE -

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Basic information

Entry
Database: PDB / ID: 1an9
TitleD-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE
ComponentsD-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / FAD / OXIDASE / D-AMINO ACID / FLAVOPROTEIN
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
2-AMINOBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.5 Å
AuthorsMiura, R. / Setoyama, C. / Nishina, Y. / Shiga, K. / Mizutani, H. / Miyahara, I. / Hirotsu, K.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.
Authors: Miura, R. / Setoyama, C. / Nishina, Y. / Shiga, K. / Mizutani, H. / Miyahara, I. / Hirotsu, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 1996
Title: Three-Dimensional Structure of Porcine Kidney D-Amino Acid Oxidase at 3.0 A Resolution
Authors: Mizutani, H. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Miura, R.
History
DepositionJun 28, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-AMINO ACID OXIDASE
B: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0716
Polymers77,2262
Non-polymers1,8454
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-23 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.310, 92.580, 71.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-AMINO ACID OXIDASE


Mass: 38612.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PET SYSTEM / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P00371, D-amino-acid oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.3
Details: PROTEIN WAS CRYSTALLIZED FROM 120MM SODIUM ACETATE, 60MM SODIUM CITRATE, 30% PEG4000, pH 6.3
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: Setoyama, C., (1996) J. Biochem., 119, 1114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
2120 mMsodium acetate1drop
360 mMsodium citrate1drop
40.2 Msodium benzoate1drop
55 %PEG40001drop
6200 mMsodium acetate1reservoir
7100 mMsodium citrate1reservoir
830 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22424 / % possible obs: 87.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.5→2.61 Å / % possible all: 73.32
Reflection
*PLUS
Num. measured all: 66408

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1AA8

1aa8
PDB Unreleased entry


Resolution: 2.5→10 Å / Data cutoff high absF: 100000000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2165 10 %RANDOM
Rwork0.201 ---
obs0.201 21755 87.5 %-
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5458 0 126 112 5696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.522
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.85
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.561
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.345 219 7.07 %
Rwork0.2829 2051 -
obs--73.32 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.FADTOPOLOGY.FAD
X-RAY DIFFRACTION3PARAM.ANTTOPOLOGY.ANT
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.854
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.561

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