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- PDB-1c0k: CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1c0k
TitleCRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE
ComponentsPROTEIN (D-AMINO ACID OXIDASE)
KeywordsOXIDOREDUCTASE / FLAVIN CONTAINING PROTEIN / ALPHA-BETA-ALPHA MOTIF
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
FLAVIN-ADENINE DINUCLEOTIDE / LACTIC ACID / D-amino-acid oxidase
Similarity search - Component
Biological speciesRhodosporidium toruloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 Å
AuthorsUmhau, S. / Molla, G. / Diederichs, K. / Pilone, M.S. / Ghisla, S. / Welte, W. / Pollegioni, L.
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 16, 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: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_validate_chiral / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_chiral.auth_atom_id / _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: PROTEIN (D-AMINO ACID OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4913
Polymers39,6151
Non-polymers8762
Water11,223623
1
A: PROTEIN (D-AMINO ACID OXIDASE)
hetero molecules

A: PROTEIN (D-AMINO ACID OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9816
Polymers79,2302
Non-polymers1,7514
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)120.670, 120.670, 136.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 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
#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-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
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: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.46→100 Å / Num. obs: 515122 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.1
Reflection
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 100 Å / Num. obs: 83893 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Num. measured all: 515122
Reflection shell
*PLUS
% possible obs: 91.2 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
MAR345data collection
XDSdata scaling
X-PLORphasing
RefinementResolution: 1.46→100 Å / σ(F): 0
% reflectionSelection details
obs99.1 %-
Rfree-RANDOM, BUT SAME AS I IN COMLEX WITH D-ALANI
Refinement stepCycle: LAST / Resolution: 1.46→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 60 623 3482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.73
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
Lowest resolution: 100 Å / σ(F): 0 / Rfactor obs: 0.112 / Rfactor Rfree: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 1.73

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