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- PDB-1c0p: D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OC... -

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Basic information

Entry
Database: PDB / ID: 1c0p
TitleD-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES
ComponentsD-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA MOTIF / FLAVIN CONTAINING PROTEIN / OXIDASE
Function / homology
Function and homology information


D-glutamate oxidase activity / D-amino acid metabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / glycine oxidase activity / D-amino acid catabolic process / nitrogen utilization / peroxisomal matrix / FAD binding / peroxisome
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
D-ALANINE / FLAVIN-ADENINE DINUCLEOTIDE / PEROXIDE ION / D-amino-acid oxidase
Similarity search - Component
Biological speciesRhodosporidium toruloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsUmhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, S.M. / Ghisla, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
Authors: Umhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, M.S. / Ghisla, S.
History
DepositionJul 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6145
Polymers39,6151
Non-polymers9994
Water11,025612
1
A: D-AMINO ACID OXIDASE
hetero molecules

A: D-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,22710
Polymers79,2302
Non-polymers1,9978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
Unit cell
Length a, b, c (Å)120.885, 120.885, 136.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-3448-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein D-AMINO ACID OXIDASE


Mass: 39614.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodosporidium toruloides (fungus) / Plasmid: PT7.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80324, D-amino-acid oxidase

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Non-polymers , 5 types, 616 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM HEPES 200 MM AMMONIUM SULFATE 16% POLYETHYLENE GLYCOL (PEG) 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMHEPES1drop
2100 mMHEPES1reservoir
315 %PEG100001reservoir
4200 mMammonium sulfate1reservoir
51 mML-lactate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9114
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9114 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 1000770 / Num. obs: 155642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.524 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.2 Å / Num. measured all: 1000779 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementResolution: 1.2→100 Å / σ(F): 4 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.15 7895 -RANDOM AND AS IN RELATED D-AMINO ACID OXIDASE FROM YEAST RHODOTORULA GRACILIS
all0.125 147430 --
obs0.116 125938 5.3 %-
Refinement stepCycle: LAST / Resolution: 1.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 67 612 3466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.57
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 100 Å / σ(F): 4 / Rfactor obs: 0.118 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.116
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.57

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