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- PDB-2xvj: Crystal structure of the mutant bacterial flavin containing monoo... -

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Basic information

Entry
Database: PDB / ID: 2xvj
TitleCrystal structure of the mutant bacterial flavin containing monooxygenase in complex with indole
ComponentsFLAVIN-CONTAINING MONOOXYGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding / identical protein binding
Similarity search - Function
Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / INDOLE / NITRATE ION / OXYGEN MOLECULE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesMETHYLOPHAGA AMINISULFIDIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural and Functional Analysis of Bacterial Flavin-Containing Monooxygenase Reveals its Ping-Pong-Type Reaction Mechanism.
Authors: Cho, H.J. / Cho, H.Y. / Kim, K.J. / Kim, M.H. / Kim, S.W. / Kang, B.S.
History
DepositionOct 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: FLAVIN-CONTAINING MONOOXYGENASE
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,33116
Polymers162,1453
Non-polymers3,18513
Water2,540141
1
A: FLAVIN-CONTAINING MONOOXYGENASE
B: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,28511
Polymers108,0972
Non-polymers2,1899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-4.7 kcal/mol
Surface area31510 Å2
MethodPISA
2
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules

C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,09010
Polymers108,0972
Non-polymers1,9938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8440 Å2
ΔGint-0.4 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.117, 67.850, 138.899
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2016-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein FLAVIN-CONTAINING MONOOXYGENASE / NADPH OXIDASE / INDOLE OXIDASE


Mass: 54048.414 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHAGA AMINISULFIDIVORANS (bacteria)
Strain: SK1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83XK4, flavin-containing monooxygenase

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Non-polymers , 6 types, 154 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H7N
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 207 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 207 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 207 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 207 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 207 TO SER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.88 % / Description: NONE
Crystal growDetails: 15% PEG 3350 0.1 M MES PH 6.0 0.2 M AMMONIUM NITRATE

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 50468 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.64 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.48→50.01 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 14.256 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23682 2677 5.2 %RANDOM
Rwork0.19883 ---
obs0.20083 49094 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.97 Å2
2--0.33 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.48→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10841 0 216 141 11198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02111428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.94815569
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52251338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7523.813577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.059151734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8011559
X-RAY DIFFRACTIONr_chiral_restr0.0740.21578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218969
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_it0.3071.56677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.582210735
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.83634751
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3544.54832
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: 2.475→2.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 104 -
Rwork0.208 2394 -
obs--64.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04380.5829-0.02950.82770.22750.84150.0774-0.16520.17950.0302-0.12820.16470.1322-0.18320.05090.0795-0.0763-0.03410.1108-0.02030.0974-34.42-40.8140.905
21.44840.1693-0.10760.38570.1690.80170.0627-0.24670.10030.1031-0.0264-0.02270.050.1806-0.03620.0883-0.0536-0.06170.1446-0.00150.08182.091-31.94344.741
31.2233-0.1634-0.08670.49570.1550.99430.0459-0.01260.20540.0172-0.011-0.0531-0.12460.2485-0.03490.0848-0.0435-0.05820.06840.00370.104418.861-26.7350.986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 447
2X-RAY DIFFRACTION2B2 - 446
3X-RAY DIFFRACTION3C2 - 447

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