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- PDB-2uzz: X-ray structure of N-methyl-L-tryptophan oxidase (MTOX) -

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Basic information

Entry
Database: PDB / ID: 2uzz
TitleX-ray structure of N-methyl-L-tryptophan oxidase (MTOX)
ComponentsN-METHYL-L-TRYPTOPHAN OXIDASE
KeywordsOXIDOREDUCTASE / N-METHYLTRYPTOPHAN OXIDASE (MTOX) / OXIDATIVE DEMETHYLATION OF N-METHYL-L-TRYPTOPHAN / FAD / FLAVOENZYME / FLAVOPROTEIN
Function / homology
Function and homology information


N-methyl-L-amino-acid oxidase activity / Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / sarcosine oxidase activity / flavin adenine dinucleotide binding / DNA damage response / cytosol
Similarity search - Function
N-methyl-L-tryptophan oxidase MTOX / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...N-methyl-L-tryptophan oxidase MTOX / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / N-methyl-L-tryptophan oxidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsIlari, A. / Fiorillo, A. / Franceschini, S. / Bonamore, A. / Colotti, G. / Boffi, A.
CitationJournal: Proteins / Year: 2008
Title: The X-Ray Structure of N-Methyltryptophan Oxidase Reveals the Structural Determinants of Substrate Specificity.
Authors: Ilari, A. / Bonamore, A. / Franceschini, S. / Fiorillo, A. / Boffi, A. / Colotti, G.
History
DepositionMay 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-METHYL-L-TRYPTOPHAN OXIDASE
B: N-METHYL-L-TRYPTOPHAN OXIDASE
C: N-METHYL-L-TRYPTOPHAN OXIDASE
D: N-METHYL-L-TRYPTOPHAN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,19812
Polymers163,9644
Non-polymers3,2348
Water00
1
A: N-METHYL-L-TRYPTOPHAN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7993
Polymers40,9911
Non-polymers8092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: N-METHYL-L-TRYPTOPHAN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7993
Polymers40,9911
Non-polymers8092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: N-METHYL-L-TRYPTOPHAN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7993
Polymers40,9911
Non-polymers8092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: N-METHYL-L-TRYPTOPHAN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7993
Polymers40,9911
Non-polymers8092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.188, 89.809, 91.915
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 2 - 370 / Label seq-ID: 2 - 370

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.67164, 0.04414, -0.73956), (0.12779, -0.99016, 0.05696), (-0.72977, -0.13277, -0.67067)-4.59588, -22.52567, -14.40183
3given(-0.81627, -0.31025, -0.48729), (-0.11856, 0.91556, -0.38431), (0.56537, -0.25593, -0.78413)-8.97132, 14.13278, -62.50146
4given(-0.26788, -0.09316, 0.95894), (0.08556, -0.99368, -0.07263), (0.95965, 0.06259, 0.27416)6.44509, -3.73253, -49.21952

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Components

#1: Protein
N-METHYL-L-TRYPTOPHAN OXIDASE / N-METHYLTRYPTOPHAN OXIDASE / MTOX


Mass: 40990.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P40874, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.6 % / Description: NONE
Crystal growpH: 5.6
Details: PEG4000 20%, ISOPROPANOL 20%, SODIUM CITRATE 0.1 M, PH=5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97973
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 21160 / % possible obs: 92 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4 / % possible all: 93.8

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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 1EL5

1el5


Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.783 / SU B: 36.637 / SU ML: 0.635 / Cross valid method: THROUGHOUT / ESU R Free: 0.75 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1154 5 %RANDOM
Rwork0.236 ---
obs0.24 21754 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å22.76 Å2
2---0.26 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11503 0 216 0 11719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.96716408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70351478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2324.223573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.033151814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551564
X-RAY DIFFRACTIONr_chiral_restr0.1580.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029381
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.25654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.28026
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1111.57350
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.214211760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.32535067
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5474.54648
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2861 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.350.5
2Bmedium positional0.380.5
3Cmedium positional0.380.5
4Dmedium positional0.420.5
1Amedium thermal0.142
2Bmedium thermal0.142
3Cmedium thermal0.152
4Dmedium thermal0.142
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 64
Rwork0.267 1494

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