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- PDB-2jae: The structure of L-amino acid oxidase from Rhodococcus opacus in ... -

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Basic information

Entry
Database: PDB / ID: 2jae
TitleThe structure of L-amino acid oxidase from Rhodococcus opacus in the unbound state
ComponentsL-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / DIMERISATION MODE / L-AMINO ACID OXIDASE / HYDRIDE TRANSFER MECHANISM / GR2-FAMILY / FLAVOENZYME / FAD CONTAINING
Function / homology
Function and homology information


L-glutamate oxidase activity / L-lysine oxidase activity / L-phenylalaine oxidase activity / L-amino-acid oxidase / amino acid catabolic process / nucleotide binding / cytoplasm
Similarity search - Function
de novo design (two linked rop proteins) - #240 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / : / de novo design (two linked rop proteins) / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...de novo design (two linked rop proteins) - #240 / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / : / de novo design (two linked rop proteins) / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / L-amino acid oxidase
Similarity search - Component
Biological speciesRHODOCOCCUS OPACUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsFaust, A. / Niefind, K. / Hummel, W. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Structure of a Bacterial L-Amino Acid Oxidase from Rhodococcus Opacus Gives New Evidence for the Hydride Mechanism for Dehydrogenation.
Authors: Faust, A. / Niefind, K. / Hummel, W. / Schomburg, D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and Preliminary X-Ray Analysis of a Bacterial L-Amino-Acid Oxidase from Rhodococcus Opacus
Authors: Faust, A. / Geueke, B. / Niefind, K. / Hummel, W. / Schomburg, D.
History
DepositionNov 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,3954
Polymers106,8242
Non-polymers1,5712
Water17,889993
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.696, 109.705, 134.402
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 L-AMINO ACID OXIDASE


Mass: 53411.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 46-534 / Source method: isolated from a natural source / Details: DSM 43250 / Source: (natural) RHODOCOCCUS OPACUS (bacteria) / References: UniProt: Q8VPD4, L-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growpH: 7.8 / Details: 100MM HEPES PH 7.8 10% 2-PROPANOL 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.816
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.816 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 290588 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.4
Reflection shellResolution: 1.21→1.22 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.9 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→15.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.032 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 13406 5 %RANDOM
Rwork0.152 ---
obs0.154 252619 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.25→15.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 0 106 993 8496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.060.0217674
X-RAY DIFFRACTIONr_bond_other_d0.0010.025183
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.95710381
X-RAY DIFFRACTIONr_angle_other_deg1.069312535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.923.571364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.668151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851556
X-RAY DIFFRACTIONr_chiral_restr0.0620.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.028676
X-RAY DIFFRACTIONr_gen_planes_other0.2210.021654
X-RAY DIFFRACTIONr_nbd_refined0.2020.21515
X-RAY DIFFRACTIONr_nbd_other0.1660.25625
X-RAY DIFFRACTIONr_nbtor_refined0.180.23836
X-RAY DIFFRACTIONr_nbtor_other0.0820.23729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1560.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 974
Rwork0.211 18255

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