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- PDB-8b2d: CRYSTAL STRUCTURE OF BACTERIAL FLAVIN CONTAINING MONOOXYGENASE TH... -

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Basic information

Entry
Database: PDB / ID: 8b2d
TitleCRYSTAL STRUCTURE OF BACTERIAL FLAVIN CONTAINING MONOOXYGENASE THERMORESISTANT MUTANT, IN COMPLEX WITH NADP+
ComponentsFlavin-containing monooxygenase, Fmo
KeywordsOXIDOREDUCTASE / thermoresistant mutant / complex / flavin adenine dinucleotide / nicotinamide adenine dinucleotide phosphate
Function / homology
Function and homology information


flavin-containing monooxygenase / hypotaurine dehydrogenase activity / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin-containing monooxygenase, Fmo
Similarity search - Component
Biological speciesMethylophaga aminisulfidivorans MP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J. / Ferrer Martinez, M. / Goris, M. / Bjerga, G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105838RB-C33 Spain
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Increased Thermostability of an Engineered Flavin-Containing Monooxygenase to Remediate Trimethylamine in Fish Protein Hydrolysates.
Authors: Goris, M. / Cea-Rama, I. / Puntervoll, P. / Ree, R. / Almendral, D. / Sanz-Aparicio, J. / Ferrer, M. / Bjerga, G.E.K.
History
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-containing monooxygenase, Fmo
B: Flavin-containing monooxygenase, Fmo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,34517
Polymers108,2632
Non-polymers4,08315
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA Analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-66 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.606, 130.361, 115.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-503-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 444 / Label seq-ID: 2 - 444

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flavin-containing monooxygenase, Fmo


Mass: 54131.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_00532 / Production host: Escherichia coli MC1061 (bacteria)
References: UniProt: F5SYD3, flavin-containing monooxygenase

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Non-polymers , 7 types, 510 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2M (NH4)SO4, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2020 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 1.62→45.27 Å / Num. obs: 120046 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Net I/σ(I): 20.7
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 5926 / CC1/2: 0.898 / Rpim(I) all: 0.22

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XVE

2xve


Resolution: 1.62→45.27 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.505 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1797 6049 5 %RANDOM
Rwork0.1616 ---
obs0.1625 113948 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.57 Å2 / Biso mean: 21.524 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0 Å2
2--0.57 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.62→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7337 0 264 495 8096
Biso mean--24.92 28.25 -
Num. residues----892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176830
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.65510696
X-RAY DIFFRACTIONr_angle_other_deg1.4461.58415789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50622.528451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.371151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6031544
X-RAY DIFFRACTIONr_chiral_restr0.080.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021915
Refine LS restraints NCS

Ens-ID: 1 / Number: 15825 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 416 -
Rwork0.207 8361 -
all-8777 -
obs--99.91 %

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