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- PDB-2jb3: The structure of L-amino acid oxidase from Rhodococcus opacus in ... -

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Basic information

Entry
Database: PDB / ID: 2jb3
TitleThe structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate
ComponentsL-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / L-AMINO ACID OXIDASE / HYDRIDE TRANSFER MECHANISM / GR2-FAMILY / FLAVOENZYME / FAD CONTAINING / INHIBITOR COMPLEX / DIMERISATION MODE
Function / homology
Function and homology information


L-glutamate oxidase activity / L-phenylalaine oxidase activity / L-lysine oxidase activity / L-amino-acid oxidase / nucleotide binding / cytoplasm
Similarity search - Function
de novo design (two linked rop proteins) - #240 / de novo design (two linked rop proteins) / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...de novo design (two linked rop proteins) - #240 / de novo design (two linked rop proteins) / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / 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
2-AMINOBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / L-amino acid oxidase
Similarity search - Component
Biological speciesRHODOCOCCUS OPACUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionDec 1, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)108,6696
Polymers106,8242
Non-polymers1,8454
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.649, 109.676, 134.368
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 / 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 / Anthranilic acid


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8 / Details: 100MM HEPES PH 7.8 10% 2-PROPANOLE 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9195
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 83174 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JAE

2jae


Resolution: 1.85→19.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.643 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.538 / ESU R Free: 0.133
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NON-PLANAR FAD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4145 5 %RANDOM
Rwork0.151 ---
obs0.154 78881 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 126 985 8506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217693
X-RAY DIFFRACTIONr_bond_other_d0.0020.025200
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.95910402
X-RAY DIFFRACTIONr_angle_other_deg1.385312566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67423.571364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.529151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8351556
X-RAY DIFFRACTIONr_chiral_restr0.0840.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0510.028697
X-RAY DIFFRACTIONr_gen_planes_other0.2190.021673
X-RAY DIFFRACTIONr_nbd_refined0.2180.21572
X-RAY DIFFRACTIONr_nbd_other0.1840.25780
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23776
X-RAY DIFFRACTIONr_nbtor_other0.0860.23951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2841
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.441.56010
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83727482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.03333646
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0444.52920
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 297
Rwork0.166 5621

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