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- PDB-3zdn: D11-C mutant of monoamine oxidase from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 3zdn
TitleD11-C mutant of monoamine oxidase from Aspergillus niger
ComponentsMONOAMINE OXIDASE N
KeywordsOXIDOREDUCTASE / FLAVIN DEPENDENT OXIDASE / AMINES
Function / homology
Function and homology information


monoamine oxidase / monoamine oxidase activity / peroxisome
Similarity search - Function
: / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...: / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Monoamine oxidase N
Similarity search - Component
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFrank, A. / Ghislieri, D. / Willies, S. / Turner, N.J. / Grogan, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Engineering an Enantioselective Amine Oxidase for the Synthesis of Pharmaceutical Building Blocks and Alkaloid Natural Products.
Authors: Ghislieri, D. / Green, A.P. / Pontini, M. / Willies, S.C. / Rowles, I. / Frank, A. / Grogan, G. / Turner, N.J.
History
DepositionNov 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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_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_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: MONOAMINE OXIDASE N
B: MONOAMINE OXIDASE N
C: MONOAMINE OXIDASE N
D: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,85912
Polymers221,4684
Non-polymers3,3908
Water9,710539
1
A: MONOAMINE OXIDASE N
B: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4296
Polymers110,7342
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-5.6 kcal/mol
Surface area30410 Å2
MethodPISA
2
C: MONOAMINE OXIDASE N
D: MONOAMINE OXIDASE N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4296
Polymers110,7342
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-5.9 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.600, 119.340, 178.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 486
2114B1 - 486
3114C1 - 486
4114D1 - 486

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.799619, 0.594674, -0.083496), (0.596463, 0.77041, -0.225166), (-0.069574, -0.22985, -0.970736)-16.17418, 8.84494, 26.35791
3given(-0.142732, -0.163862, 0.976103), (-0.156604, -0.970038, -0.185744), (0.977294, -0.179373, 0.112794)-59.8098, -104.71661, 35.42658
4given(-0.052889, -0.430425, -0.901075), (-0.430185, -0.804498, 0.409542), (-0.90119, 0.409289, -0.142613)-33.19079, -115.60168, 20.49133

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Components

#1: Protein
MONOAMINE OXIDASE N / AMINE OXIDASE MAO-N


Mass: 55367.062 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P46882, monoamine oxidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS AS LISTED [I246T, N336S, M348K, T384N, D385S, F210E, L213T, M242Q, W430G]

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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: 2.6 Å3/Da / Density % sol: 52.8 % / Description: NONE
Crystal growpH: 7
Details: 22% (W/V) PEG3350, 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE AT PH 7.0 AND 200 MM PROLINE.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→99.26 Å / Num. obs: 96920 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.55→2.63 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVM

2vvm


Resolution: 2.55→99.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.473 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21428 3836 5 %RANDOM
Rwork0.15267 ---
obs0.15576 72593 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.55→99.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14793 0 228 539 15560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01915419
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.94220966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7251896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94522.784704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.188152308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60315118
X-RAY DIFFRACTIONr_chiral_restr0.1150.22243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111910
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3652 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.230.5
2Bmedium positional0.220.5
3Cmedium positional0.240.5
4Dmedium positional0.250.5
1Amedium thermal6.832
2Bmedium thermal4.692
3Cmedium thermal5.082
4Dmedium thermal6.722
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 282 -
Rwork0.194 5293 -
obs--100 %

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