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- PDB-2vqb: Bacterial flavin-containing monooxygenase in complex with NADP: s... -

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Basic information

Entry
Database: PDB / ID: 2vqb
TitleBacterial flavin-containing monooxygenase in complex with NADP: soaking in aerated solution
ComponentsFLAVIN-CONTAINING MONOOXYGENASE
KeywordsOXIDOREDUCTASE / NADP / OXYGEN / FLAVIN / DRUG METABOLISM
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXYGEN MOLECULE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesMETHYLOPHAGA SP. SK1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlfieri, A. / Malito, E. / Orru, R. / Fraaije, M.W. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Revealing the Moonlighting Role of Nadp in the Structure of a Flavin-Containing Monooxygenase.
Authors: Alfieri, A. / Malito, E. / Orru, R. / Fraaije, M.W. / Mattevi, A.
History
DepositionMar 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2008Provider: 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 / 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_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_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

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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
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,83028
Polymers213,3634
Non-polymers7,46724
Water00
1
A: FLAVIN-CONTAINING MONOOXYGENASE
D: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,41514
Polymers106,6822
Non-polymers3,73312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-15.6 kcal/mol
Surface area38190 Å2
MethodPQS
2
B: FLAVIN-CONTAINING MONOOXYGENASE
C: FLAVIN-CONTAINING MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,41514
Polymers106,6822
Non-polymers3,73312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18.4 kcal/mol
Surface area38220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)218.665, 218.665, 130.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA8 - 2488 - 248
21THRTHRGLUGLUBB8 - 2488 - 248
31THRTHRGLUGLUCC8 - 2488 - 248
41THRTHRGLUGLUDD8 - 2488 - 248
12PROPRONAPNAPAA - F250 - 501250
22PROPRONAPNAPBB - L250 - 501250
32PROPRONAPNAPCC - R250 - 501250
42PROPRONAPNAPDD - X250 - 501250

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FLAVIN-CONTAINING MONOOXYGENASE


Mass: 53340.754 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOPHAGA SP. SK1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q83XK4

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Non-polymers , 5 types, 24 molecules

#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 153 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 154 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 153 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 154 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 153 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 154 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 153 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 154 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 153 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 154 TO ALA
Nonpolymer detailsOXYGEN MOLECULE (OXY): THE ELECTRON DENSITY SHOWS A PEAK THAT HAS BEEN TENTATIVELY ASSIGNED TO A ...OXYGEN MOLECULE (OXY): THE ELECTRON DENSITY SHOWS A PEAK THAT HAS BEEN TENTATIVELY ASSIGNED TO A DIOXYGEN MOLECULE. WE CANNOT EXCLUDE THAT, INSTEAD OF DIOXYGEN, A SUPEROXIDE MOLECULE OR A MONOATOMIC CATION IS PRESENT.

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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: 4.28 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% W/V PEG4000, 100 MM NA-HEPES, 1 MM NADP PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 86940 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQ7

2vq7


Resolution: 2.8→29.72 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.911 / SU B: 26.134 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4332 5 %RANDOM
Rwork0.226 ---
obs0.226 82568 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å2-0.96 Å20 Å2
2---1.93 Å20 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14552 0 484 0 15036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02215516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.96621136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6251768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63823.744780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.124152408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3281584
X-RAY DIFFRACTIONr_chiral_restr0.0990.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.26997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.210402
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5541.59017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.982214248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3237904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.174.56888
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: 3728 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
1Atight thermal0.070.5
2Btight thermal0.070.5
3Ctight thermal0.070.5
4Dtight thermal0.060.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 338
Rwork0.374 5909

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