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- PDB-2jb2: The structure of L-amino acid oxidase from Rhodococcus opacus in ... -

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Basic information

Entry
Database: PDB / ID: 2jb2
TitleThe structure of L-amino acid oxidase from Rhodococcus opacus in complex with L-phenylalanine.
ComponentsL-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / SUBSTRATE COMPLEX / L-AMINO ACID OXIDASE / NON-PLANAR FAD / DIMERISATION MODE / GR2-FAMILY / FLAVOENZYME / FAD CONTAINING / HYDRIDE TRANSFER MECHANISM
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 / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. ...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 / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 / PHENYLALANINE / L-amino acid oxidase
Similarity search - Component
Biological speciesRHODOCOCCUS OPACUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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)108,7256
Polymers106,8242
Non-polymers1,9014
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.053, 110.059, 134.530
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-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 1.45→30 Å / Num. obs: 157853 / % possible obs: 91.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 86.1

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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: 1.45→14.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.198 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAD IS NON-PLANAR
RfactorNum. reflection% reflectionSelection details
Rfree0.199 7886 5 %RANDOM
Rwork0.172 ---
obs0.173 149605 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 0 130 711 8238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217713
X-RAY DIFFRACTIONr_bond_other_d0.0010.025212
X-RAY DIFFRACTIONr_angle_refined_deg1.121.95710436
X-RAY DIFFRACTIONr_angle_other_deg1.088312604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94623.587368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.122151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9551556
X-RAY DIFFRACTIONr_chiral_restr0.0660.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0460.028727
X-RAY DIFFRACTIONr_gen_planes_other0.2280.021671
X-RAY DIFFRACTIONr_nbd_refined0.2060.21452
X-RAY DIFFRACTIONr_nbd_other0.1670.25466
X-RAY DIFFRACTIONr_nbtor_refined0.180.23778
X-RAY DIFFRACTIONr_nbtor_other0.0810.23712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2508
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9811.56073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17527514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74133674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.44.52920
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: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 506
Rwork0.162 10071

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