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- PDB-2xve: Crystal structure of bacterial flavin-containing monooxygenase -

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Basic information

Entry
Database: PDB / ID: 2xve
TitleCrystal structure of bacterial flavin-containing monooxygenase
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 / NITRATE ION / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesMETHYLOPHAGA AMINISULFIDIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)164,46912
Polymers162,3743
Non-polymers2,0959
Water13,421745
1
A: FLAVIN-CONTAINING MONOOXYGENASE
B: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4058
Polymers108,2492
Non-polymers1,1566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-13.6 kcal/mol
Surface area32560 Å2
MethodPISA
2
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules

C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1288
Polymers108,2492
Non-polymers1,8796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7340 Å2
ΔGint-26.8 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.225, 68.991, 140.529
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 54124.512 Da / Num. of mol.: 3
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, EC: 1.14.13.8
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growDetails: 10% PEG 3350, 0.2 M AMMONIUM NITRATE

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 99129 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.59 / % possible all: 85.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→50.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.815 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4942 5 %RANDOM
Rwork0.17 ---
obs0.172 94173 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.27 Å2
2--0.03 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10889 0 140 745 11774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.891.94715728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05651364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34723.868592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.573151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3821561
X-RAY DIFFRACTIONr_chiral_restr0.0640.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219060
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_it0.2121.56714
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.399210820
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53634824
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8584.54892
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: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.138 293 -
Rwork0.109 5446 -
obs--74.44 %
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)
11.90570.3092-0.17120.4270.01840.85410.0575-0.01890.0250.0291-0.0108-0.0422-0.08950.0946-0.04670.1338-0.0245-0.0380.0126-0.00350.149833.765641.7702-28.6378
21.32290.035-0.13930.4304-0.21791.01170.00540.0515-0.02450.0707-0.03790.0003-0.0475-0.16080.03240.0788-0.0043-0.02580.041-0.01460.0601-2.679333.0331-25.2297
30.9557-0.29680.06850.40710.09771.1697-0.0406-0.0583-0.1230.02120.00280.06980.216-0.22550.03780.1089-0.0537-0.00170.1464-0.00230.0235-18.460326.7218-69.469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 447
2X-RAY DIFFRACTION2B2 - 447
3X-RAY DIFFRACTION3C2 - 445

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